Data Import and Processing

Methods

The differential gene expression and gene set analyses were performed in RStudio (Posit team (2023), version 2023.6.2.561, R version 4.3.2 (2023-10-31)).

Differential Transcript Usage Analysis

After detecting differentially expressed genes, differentially expressed isoforms were identified using Differential Transcript Usage (DTU) analysis pipeline using DRIMSeq and DEXSeq libraries. DTU complements DGE as it enables the identification of alternative splicing and isoform switches even if the gene expression does not change between conditions [1, 2]. As for DGE, the aim was to identify differentially expressed isoforms in samples generated over course of the 5 days and to compare the results of the differential gene expression analysis of the Illumina+Salmon data (short read data) with the results of the PacBio+Bambu data (long read data). To do so, in total 8 different count data frames were analyzed. For each of the 4 NDR cutoffs (0.025, 0.05, 0.1, 0.2), there are two different count data frames, one derived from Illumina+Salmon and one derived from PacBio+Bambu. I didn’t change this - I think we can unite DGE and DTU and write that both were conducted - the first two sentences I wrote can just be added after the first sentence of Michel.

The inspiration for this protocol was taken from:

https://ycl6.gitbook.io/guide-to-rna-seq-analysis/differential-expression-analysis/differential-transcript-usage/dtu-using-dexseq

https://www.bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html

References

[1] Marques-Coelho, D., Iohan, L.d.C.C., Melo de Farias, A.R. et al. Differential transcript usage unravels gene expression alterations in Alzheimer’s disease human brains. npj Aging Mech Dis 7, 2 (2021). https://doi.org/10.1038/s41514-020-00052-5

[2] https://www.bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html

[3] Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111.

[4] Nowicka M, Robinson MD. DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics. F1000Res. 2016 Jun 13;5:1356. doi: 10.12688/f1000research.8900.2.

Load packages

library(tidyverse)
library(ggvenn)
library(DRIMSeq)
library(DEXSeq)
library(stageR)
library(stringr)
library(ggplot2)
library(ggbeeswarm)
library(UpSetR)
library(viridis)

Load data

The data is loaded from RDS-objects that have been created with the import_processing.qmd file. For each of the 4 NDR cutoffs (0.025, 0.05, 0.1, 0.2), two data frames exist containing the expression data (counts) of the two different technologies used to obtain the data:

Illumina sequencing and Salmon quantification (short read)
PacBio sequencing and Bambu quantification (long read)

In total, this adds up to 8 different data frames. Each of these data frames contains 11 samples, which are replicates from one of five different time points. Each time point has 1-3 replicates.

Load data

df_list_bambu <- readRDS("./bambu.rds")
df_list_salmon <- readRDS("./salmon.rds")
df_list_meta <- readRDS("./meta.rds")

## Salmon
salmon_0.025 <- df_list_salmon$salmon_0.025
salmon_0.05 <- df_list_salmon$salmon_0.05
salmon_0.1 <- df_list_salmon$salmon_0.1
salmon_0.2 <- df_list_salmon$salmon_0.2
## Bambu
bambu_0.025 <- df_list_bambu$bambu_0.025
bambu_0.05 <- df_list_bambu$bambu_0.05
bambu_0.1 <- df_list_bambu$bambu_0.1
bambu_0.2 <- df_list_bambu$bambu_0.2

Testing Pipeline

The workflow was taken from and tested on the given dataset. The workflow makes use of 3 libraries vignettes: DRIMSeq, DEXSeq and stageR

DEXSeq assumes that the feature (transcript) counts follow a negative binomial (NB) distribution and considers them as relative proportions of the group (the gene) using an interaction term in a generalized linear model (GLM) [2, 3]. DRIMSeq assumes that feature proportions follow the Dirichlet distribution (an Dirichlet Multinomial model (MD) for each gene) where the total count for the gene is considered fixed [2, 4].

salmon_0.025

Here, I considered using tximport library for salmon data, however, I realized that it has not been adapted for Bambu data and decided to leave it at counts (the same as in DGE).

library(tximport)
txi <- tximport(c("/home/annatoidze/Documents/ETHZ/STA426/project/data/0.1_salmon_day0-rep1/quant.sf"), type="salmon", txOut=TRUE,
                countsFromAbundance="scaledTPM")
cts <- txi$counts
cts <- cts[rowSums(cts) > 0,]
patterns_to_remove <- c("^DQ", "^EF", "^SIRV")
cts <- data.frame(cts)
cts <-
  cts[!grepl(paste(patterns_to_remove, collapse = "|"),
                      rownames(cts)), , drop =F]

It is checked how many reads (the range) that mapped to transcriptome using salmon. Also, txdf dataframe is created which maps transcripts to corresponding genes.

range(colSums(salmon_0.025)/1e6) # Between 14.24 and 93.31 million reads mapped to transcriptome based on the replicate

[1] 13.65181 90.11048

# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.025
all(rownames(salmon_0.025) %in% rownames(txdf))

[1] TRUE

The samps dataframe relates the sample identifiers to the conditions (in this case, day of the experiment). The cts dataframe corresponds to the counts. In order to run DRIMSeq, a dataframe counts with the gene ID, the feature (transcript) ID, and then columns for each of the samples is built:

samps <- df_list_meta$metadata
samps <- samps %>% column_to_rownames(var="sampleID")
colnames(samps) <- c("sample_id", "day")
samps$day <- factor(samps$day)
cts <- salmon_0.025
colnames(cts) <- samps$sample_id
counts <- data.frame(gene_id=txdf$gene_id,
                     feature_id=rownames(txdf),
                     cts)

DRIMSeq

We create a dmDSdata object with previously generated dataframes.

d <- dmDSdata(counts=counts, samples=samps)
d

An object of class dmDSdata 
with 61603 genes and 11 samples
* data accessors: counts(), samples()

As the rows of the object are gene oriented, the genes can by checked by rows (sometimes for than one transcript mapped, thus >1 rows shown even if selecting just one):

counts(d[1,])

            gene_id        feature_id day0.rep1 day0.rep2 day0.rep3 day1.rep1
1 ENSG00000279457.4          BambuTx1   367.532   184.699   410.608   685.231
2 ENSG00000279457.4 ENST00000623083.4     0.000     0.000     0.000     0.000
  day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2 day5.rep3
1   436.705    118.02   198.441   867.349    517.19   429.408   492.926
2     0.000      0.00     0.000     0.000      0.00     0.000     0.000

Filtering

The filtering is done using the function dmFilter from DRIMSeq package. n is defined as the minimal number of samples where the genes should be expressed. n.small is the minimal number of samples where the features should be expressed. Both are set to 3, as that is the number of replicates for day 0 and 5. Additional filters are also added: for a transcript to be retained in the dataset, it is required that (1) it has a count of at least 10 in at least n.small samples, (2) it has a relative abundance proportion of at least 0.1 in at least n.small samples, and (3) the total count of the corresponding gene is at least 10 in all n samples.

n <- 3
n.small <- 3
d <- dmFilter(d,
              min_samps_feature_expr=n.small, min_feature_expr=10,
              min_samps_feature_prop=n.small, min_feature_prop=0.1,
              min_samps_gene_expr=n, min_gene_expr=10)
d

An object of class dmDSdata 
with 9901 genes and 11 samples
* data accessors: counts(), samples()

plotData(d)

It can be seen how many of the remaining genes have N isoforms.

table(table(counts(d)$gene_id))

   2    3    4    5    6    7    8    9 
5214 2887 1213  433  114   29    8    3 

Creating design matrix

The design matrix is created in a way that the first time point, day0, is used as a baseline (intercept of the model).

design_full <- model.matrix(~day, data=DRIMSeq::samples(d))
colnames(design_full)

[1] "(Intercept)" "day1"        "day2"        "day3"        "day4"       
[6] "day5"       

Precision calculation

dmPrecision is used t estimate the precision by maximum likelihood. It is inversely related to the dispersion in the DM model via following relation: \(dispersion = \frac{1}{1 + precision}\). dmFit is used to fit regression coefficients and estimate feature propotrions for each sample. dmTest is used to perform null hypothesis likelihood ratio testing on day5. plotPrecision is used to plot precision (y-axis) against mean expression (x-axis). In RNA-seq data there is usually a trend of decrease of dispersion (here, increase of precision) with increase of mean expression. This is the trend observed here.

system.time({
  d <- dmPrecision(d, design=design_full)
  d <- dmFit(d, design=design_full)
})

! Using a subset of 0.1 genes to estimate common precision !

! Using common_precision = 21.2862 as prec_init !

! Using loess fit as a shrinkage factor !

   user  system elapsed 
982.117   6.527 991.579 

plotPrecision(d)

# Numeric vector of mean gene expression.
head(mean_expression(d))

             gene_id mean_expression
1 ENSG00000052841.15       4246.4306
2  ENSG00000256591.5        377.4107
3  ENSG00000255471.1        108.7104
4 ENSG00000149328.15        174.1209
5 ENSG00000111186.13       3568.7414
6 ENSG00000111224.14        860.1869

# Numeric value of estimated common precision.
common_precision(d)

[1] 21.28624

# Numeric vector of estimated gene-wise precisions.
head(genewise_precision(d))

             gene_id genewise_precision
1 ENSG00000052841.15          70.800532
2  ENSG00000256591.5          27.737903
3  ENSG00000255471.1                 NA
4 ENSG00000149328.15                 NA
5 ENSG00000111186.13           5.373339
6 ENSG00000111224.14          11.627499

## Get fitted proportions - estimated feature ratios for each sample
head(proportions(d))

             gene_id         feature_id day0.rep1 day0.rep2 day0.rep3 day1.rep1
1 ENSG00000052841.15         BambuTx100 0.1839865 0.1839865 0.1839865 0.1985653
2 ENSG00000052841.15  ENST00000039989.9 0.5718858 0.5718858 0.5718858 0.5620527
3 ENSG00000052841.15 ENST00000299240.10 0.2441277 0.2441277 0.2441277 0.2393820
4  ENSG00000256591.5         BambuTx102 0.3369753 0.3369753 0.3369753 0.4484651
5  ENSG00000256591.5  ENST00000536670.5 0.4133106 0.4133106 0.4133106 0.3925292
6  ENSG00000256591.5  ENST00000541135.5 0.2497141 0.2497141 0.2497141 0.1590057
  day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2 day5.rep3
1 0.1146795 0.2187214 0.2187214 0.1995248 0.2203314 0.2203314 0.2203314
2 0.5777165 0.5230367 0.5230367 0.5293489 0.5704172 0.5704172 0.5704172
3 0.3076040 0.2582419 0.2582419 0.2711263 0.2092514 0.2092514 0.2092514
4 0.3755887 0.4164650 0.4164650 0.4029053 0.4589542 0.4589542 0.4589542
5 0.3137564 0.3564449 0.3564449 0.2214526 0.2033833 0.2033833 0.2033833
6 0.3106549 0.2270901 0.2270901 0.3756421 0.3376625 0.3376625 0.3376625

## Get the DM regression coefficients (gene-level) 
head(coefficients(d))

             gene_id         feature_id X.Intercept.        day1       day2
1 ENSG00000052841.15         BambuTx100   -0.2828292 0.095886410 -0.7038428
2 ENSG00000052841.15  ENST00000039989.9    0.8512479 0.002287141 -0.2209780
3 ENSG00000052841.15 ENST00000299240.10    0.0000000 0.000000000  0.0000000
4  ENSG00000256591.5         BambuTx102    0.2996931 0.737197903 -0.1098811
5  ENSG00000256591.5  ENST00000536670.5    0.5038826 0.399788318 -0.4939482
6  ENSG00000256591.5  ENST00000541135.5    0.0000000 0.000000000  0.0000000
         day3        day4        day5
1  0.11673115 -0.02381714  0.33442514
2 -0.14549291 -0.18218494  0.15158352
3  0.00000000  0.00000000  0.00000000
4  0.30676255 -0.22962832  0.00721034
5 -0.05304971 -1.03231098 -1.01083724
6  0.00000000  0.00000000  0.00000000

## Get the BB regression coefficients (feature-level) 
head(coefficients(d), level = "feature")

             gene_id         feature_id X.Intercept.        day1       day2
1 ENSG00000052841.15         BambuTx100   -0.2828292 0.095886410 -0.7038428
2 ENSG00000052841.15  ENST00000039989.9    0.8512479 0.002287141 -0.2209780
3 ENSG00000052841.15 ENST00000299240.10    0.0000000 0.000000000  0.0000000
4  ENSG00000256591.5         BambuTx102    0.2996931 0.737197903 -0.1098811
5  ENSG00000256591.5  ENST00000536670.5    0.5038826 0.399788318 -0.4939482
6  ENSG00000256591.5  ENST00000541135.5    0.0000000 0.000000000  0.0000000
         day3        day4        day5
1  0.11673115 -0.02381714  0.33442514
2 -0.14549291 -0.18218494  0.15158352
3  0.00000000  0.00000000  0.00000000
4  0.30676255 -0.22962832  0.00721034
5 -0.05304971 -1.03231098 -1.01083724
6  0.00000000  0.00000000  0.00000000

Testing and results

## Fit null model proportions and perform the LR test to detect DTU
d <- dmTest(d, coef="day5")

## Plot the gene-level p-values
plotPValues(d)

## Get the gene-level results
## Plot feature proportions for a top DTU gene
res <- DRIMSeq::results(d)
res <- res[order(res$pvalue, decreasing = FALSE), ]

### Get the feature-level results
res.txp <- DRIMSeq::results(d, level="feature")
res.txp <- res.txp[order(res.txp$pvalue, decreasing = FALSE), ]

# Significant gene results
idx <- which(res$adj_pvalue < 0.05)
res[idx,]

                gene_id         lr df       pvalue   adj_pvalue
7368 ENSG00000112759.19 288.822065  1 8.978826e-65 6.940632e-61
3863 ENSG00000171634.19 256.560124  3 2.493989e-55 9.639269e-52
1659 ENSG00000129422.15 199.630166  3 5.070757e-43 1.306565e-39
4889 ENSG00000107554.17 181.014518  2 4.933975e-40 9.534906e-37
4023 ENSG00000172889.16 157.899284  1 3.255727e-36 5.033354e-33
4219 ENSG00000164587.13 156.329510  2 1.131041e-34 1.457157e-31
8991 ENSG00000151967.18 141.167717  2 2.217276e-31 2.448507e-28
2487 ENSG00000145555.15 138.229088  3 9.105068e-30 8.797772e-27
5509 ENSG00000165629.20 127.371874  1 1.540307e-29 1.322952e-26
1834 ENSG00000026508.21 130.267177  2 5.162284e-29 3.990445e-26
3780 ENSG00000143344.16 118.855868  1 1.126227e-27 7.914302e-25
7381 ENSG00000159658.15 122.200476  2 2.914095e-27 1.877163e-24
5419 ENSG00000186635.15 130.017735  4 3.860201e-27 2.295335e-24
1345 ENSG00000134853.12 113.834644  1 1.416411e-26 7.820610e-24
2803 ENSG00000154380.18 125.840041  4 3.018695e-26 1.555634e-23
5579 ENSG00000093167.18 113.993210  2 1.764773e-25 8.526060e-23
70   ENSG00000153046.18 111.888520  2 5.054946e-25 2.298514e-22
1669 ENSG00000055118.17 114.251722  3 1.334067e-24 5.729078e-22
2833 ENSG00000155307.19 103.970834  2 2.648624e-23 1.077572e-20
6058 ENSG00000125354.24 109.958560  4 7.427273e-23 2.870641e-20
5809 ENSG00000148498.16 112.036216  5 1.520819e-22 5.598064e-20
7142 ENSG00000027869.12  98.636826  2 3.813164e-22 1.339807e-19
1919 ENSG00000115318.12 100.329400  3 1.320284e-21 4.437304e-19
7884 ENSG00000196139.14  99.018780  3 2.526186e-21 8.136425e-19
7584 ENSG00000001497.18  98.031668  3 4.117953e-21 1.273271e-18
7330 ENSG00000024526.17  88.210201  1 5.885560e-21 1.749822e-18
6140 ENSG00000090989.18  91.830058  2 1.146453e-20 3.282253e-18
413  ENSG00000102471.15  91.311997  2 1.485429e-20 4.100844e-18
7594  ENSG00000204301.6  93.569817  3 3.746705e-20 9.986907e-18
5513 ENSG00000065613.15  82.109116  1 1.287773e-19 3.318162e-17
4780 ENSG00000119335.18  83.375116  2 7.858211e-19 1.959483e-16
6867 ENSG00000196549.13  89.788185  4 1.460495e-18 3.528009e-16
7061 ENSG00000143469.20  80.949365  2 2.642827e-18 6.190623e-16
897  ENSG00000076248.11  70.375453  1 4.902620e-17 1.114625e-14
5813 ENSG00000125170.11  74.942531  2 5.326430e-17 1.146762e-14
736  ENSG00000003436.16  78.878403  3 5.340678e-17 1.146762e-14
6795 ENSG00000168918.14  73.440537  2 1.128730e-16 2.358130e-14
5739 ENSG00000069869.17  67.122199  1 2.551887e-16 5.191076e-14
2456 ENSG00000144908.14  71.119619  2 3.602227e-16 7.139798e-14
3120 ENSG00000007392.17  74.460026  3 4.729680e-16 9.140106e-14
3274 ENSG00000163923.10  65.339936  1 6.303099e-16 1.188365e-13
2673 ENSG00000038274.17  64.847789  1 8.091282e-16 1.489181e-13
2151 ENSG00000079102.16  75.194602  4 1.812410e-15 3.258123e-13
5855 ENSG00000185630.19  65.937890  2 4.805838e-15 8.442984e-13
8057 ENSG00000141376.23  64.652763  2 9.137576e-15 1.569632e-12
7754 ENSG00000147044.23  70.220599  4 2.039021e-14 3.426442e-12
2921 ENSG00000187672.14  58.031448  1 2.579608e-14 4.242631e-12
3580 ENSG00000167766.20  63.555153  3 1.021805e-13 1.645532e-11
5426 ENSG00000186439.14  59.349197  2 1.295644e-13 2.043944e-11
6891 ENSG00000138326.21  54.629751  1 1.455160e-13 2.214643e-11
8865 ENSG00000179715.13  59.108767  2 1.461149e-13 2.214643e-11
1310 ENSG00000134001.15  62.550704  3 1.675433e-13 2.490596e-11
5340 ENSG00000185187.13  62.419469  3 1.787237e-13 2.606669e-11
1871 ENSG00000115109.14  58.189938  2 2.313212e-13 3.311320e-11
2453 ENSG00000144857.15  61.156627  3 3.327391e-13 4.676497e-11
2384 ENSG00000143382.16  56.963532  2 4.270966e-13 5.895459e-11
5639 ENSG00000107938.18  56.333866  2 5.851354e-13 7.935257e-11
4875 ENSG00000137868.19  59.667195  3 6.923808e-13 9.227765e-11
8509  ENSG00000225783.9  55.859878  2 7.416204e-13 9.716484e-11
4640 ENSG00000134954.14  55.063671  2 1.104271e-12 1.422670e-10
6489 ENSG00000164209.17  61.224489  4 1.603712e-12 2.032245e-10
300  ENSG00000204314.12  60.301981  4 2.506474e-12 3.125007e-10
4440 ENSG00000060237.19  56.304381  3 3.617327e-12 4.438403e-10
2407 ENSG00000143947.15  48.163361  1 3.921477e-12 4.736409e-10
9094 ENSG00000135253.16  55.619492  3 5.064566e-12 6.022938e-10
5493 ENSG00000187147.18  46.587146  1 8.763320e-12 1.026371e-09
3238 ENSG00000163682.17  57.268406  4 1.086718e-11 1.253781e-09
6781 ENSG00000126883.18  50.337638  2 1.173061e-11 1.333495e-09
2629 ENSG00000014216.16  45.961069  1 1.206264e-11 1.351366e-09
1612 ENSG00000103723.17  53.697596  3 1.301684e-11 1.437431e-09
646  ENSG00000111321.11  45.735987  1 1.353138e-11 1.473206e-09
267  ENSG00000088305.18  45.303951  1 1.687084e-11 1.811272e-09
5915 ENSG00000008130.15  45.014710  1 1.955599e-11 2.070792e-09
3891  ENSG00000169750.9  44.465758  1 2.588451e-11 2.703882e-09
6850 ENSG00000181885.18  44.359875  1 2.732303e-11 2.816093e-09
3935 ENSG00000171992.13  44.260543  1 2.874521e-11 2.906678e-09
8143 ENSG00000109475.17  48.530627  2 2.895397e-11 2.906678e-09
4559 ENSG00000134504.14  51.255793  3 4.315147e-11 4.276421e-09
5158 ENSG00000182287.15  54.261542  4 4.639141e-11 4.539312e-09
411  ENSG00000102316.17  43.286514  1 4.728311e-11 4.545299e-09
5257 ENSG00000128951.14  47.535175  2 4.762862e-11 4.545299e-09
548  ENSG00000106484.16  42.957296  1 5.594786e-11 5.274110e-09
6460 ENSG00000079805.19  50.651255  3 5.804817e-11 5.373357e-09
9113  ENSG00000241472.7  59.443423  6 5.839095e-11 5.373357e-09
2088 ENSG00000122515.16  53.332257  4 7.260991e-11 6.603231e-09
150  ENSG00000031003.11  46.329109  2 8.704860e-11 7.824252e-09
4940 ENSG00000158560.14  46.264526  2 8.990541e-11 7.988147e-09
8562  ENSG00000243004.7  46.207683  2 9.249730e-11 8.125047e-09
4524 ENSG00000100280.17  45.761351  2 1.156243e-10 1.004242e-08
8114 ENSG00000221955.11  45.683201  2 1.202317e-10 1.032657e-08
6721 ENSG00000198561.16  48.947998  3 1.338136e-10 1.136680e-08
3391 ENSG00000165238.17  47.986410  3 2.143709e-10 1.801181e-08
5907 ENSG00000172578.12  44.448684  2 2.228901e-10 1.852625e-08
6569 ENSG00000185963.14  40.185995  1 2.308976e-10 1.894739e-08
6240 ENSG00000168734.14  44.349746  2 2.341936e-10 1.894739e-08
1788 ENSG00000101040.20  47.796198  3 2.353104e-10 1.894739e-08
2879 ENSG00000156482.11  40.085951  1 2.430306e-10 1.936728e-08
7680 ENSG00000204576.12  50.601174  4 2.704333e-10 2.133112e-08
8156 ENSG00000174428.19  47.460486  3 2.773768e-10 2.165780e-08
6107 ENSG00000036054.13  39.731681  1 2.913607e-10 2.252218e-08
3244 ENSG00000163697.17  47.266381  3 3.050458e-10 2.334657e-08
1070 ENSG00000128989.11  39.211646  1 3.802653e-10 2.881814e-08
2118 ENSG00000003147.19  46.675436  3 4.074408e-10 3.057784e-08
6256 ENSG00000143612.21  43.030122  2 4.530307e-10 3.367238e-08
354  ENSG00000075413.19  45.722319  3 6.497309e-10 4.783257e-08
757  ENSG00000115486.13  45.403177  3 7.595846e-10 5.539235e-08
2047 ENSG00000111846.20  41.624648  2 9.147925e-10 6.608734e-08
9115 ENSG00000240225.10  41.522989  2 9.624928e-10 6.888953e-08
4478 ENSG00000168259.17  37.327684  1 9.985697e-10 7.039650e-08
7918 ENSG00000101849.18  41.429603  2 1.008500e-09 7.039650e-08
2515 ENSG00000146263.12  41.424912  2 1.010868e-09 7.039650e-08
4616 ENSG00000137343.18  44.768612  3 1.036194e-09 7.151591e-08
6160 ENSG00000102181.21  37.069016  1 1.140212e-09 7.799855e-08
8796 ENSG00000119559.17  47.158885  4 1.413026e-09 9.581310e-08
8203 ENSG00000196417.13  40.541500  2 1.572263e-09 1.056834e-07
1676 ENSG00000104218.16  40.266300  2 1.804197e-09 1.202280e-07
5515 ENSG00000129353.15  39.734457  2 2.353815e-09 1.537978e-07
5078 ENSG00000101974.15  39.732969  2 2.355567e-09 1.537978e-07
2497 ENSG00000145817.17  39.722735  2 2.367650e-09 1.537978e-07
1206 ENSG00000131089.17  45.964069  4 2.505620e-09 1.614037e-07
4895 ENSG00000071054.17  51.061872  6 2.878373e-09 1.838828e-07
5245 ENSG00000151276.24  35.100401  1 3.131363e-09 1.982148e-07
636  ENSG00000110906.13  35.086375  1 3.154000e-09 1.982148e-07
65   ENSG00000164093.18  45.005544  4 3.965421e-09 2.471992e-07
1573 ENSG00000102804.15  34.523627  1 4.211087e-09 2.604136e-07
6162 ENSG00000142192.21  41.878469  3 4.257587e-09 2.611996e-07
1217 ENSG00000131477.11  38.210666  2 5.042655e-09 3.069269e-07
8408  ENSG00000242028.8  34.060451  1 5.342619e-09 3.226441e-07
5594 ENSG00000158555.15  33.905258  1 5.786210e-09 3.467241e-07
6703 ENSG00000205220.12  37.792740  2 6.214566e-09 3.695277e-07
6614 ENSG00000146540.15  37.609258  2 6.811666e-09 4.019403e-07
4279 ENSG00000180448.11  37.503004  2 7.183336e-09 4.206605e-07
5860 ENSG00000173262.12  40.781263  3 7.276363e-09 4.229044e-07
1749 ENSG00000100813.15  43.466577  4 8.279708e-09 4.776279e-07
5873 ENSG00000169398.19  37.043700  2 9.037800e-09 5.149296e-07
4240 ENSG00000137094.16  33.033262  1 9.059564e-09 5.149296e-07
934  ENSG00000124140.15  43.068162  4 1.001630e-08 5.651534e-07
9470  ENSG00000285517.1  40.080478  3 1.024466e-08 5.738496e-07
2541 ENSG00000133138.20  32.656920  1 1.099473e-08 6.114335e-07
1512 ENSG00000138162.19  36.505932  2 1.182599e-08 6.529637e-07
6094 ENSG00000124614.16  32.490224  1 1.197936e-08 6.567410e-07
7100 ENSG00000152818.19  32.370288  1 1.274199e-08 6.936310e-07
1449 ENSG00000136933.17  36.269373  2 1.331085e-08 7.155256e-07
5593 ENSG00000100099.21  45.181101  5 1.332933e-08 7.155256e-07
3360 ENSG00000164830.19  39.244966  3 1.540165e-08 8.210672e-07
5171 ENSG00000184489.13  35.853784  2 1.638513e-08 8.675139e-07
4174 ENSG00000137478.15  31.830555  1 1.682254e-08 8.846137e-07
6157 ENSG00000143369.15  31.780948  1 1.725774e-08 9.013669e-07
7244 ENSG00000162775.17  38.931935  3 1.794258e-08 9.308465e-07
6279 ENSG00000117448.14  35.212902  2 2.257436e-08 1.163332e-06
9030 ENSG00000165821.12  31.120813  1 2.424577e-08 1.241191e-06
852  ENSG00000070087.15  31.006805  1 2.571254e-08 1.307618e-06
3599 ENSG00000161551.15  34.846784  2 2.710922e-08 1.369636e-06
4613 ENSG00000143624.14  38.018613  3 2.800945e-08 1.405929e-06
3384 ENSG00000128596.17  40.808104  4 2.945295e-08 1.468847e-06
6983 ENSG00000169851.15  34.585468  2 3.089307e-08 1.530791e-06
8726  ENSG00000237515.9  30.615786  1 3.145242e-08 1.548581e-06
5755 ENSG00000164056.11  34.306420  2 3.551857e-08 1.737712e-06
1732 ENSG00000089091.16  40.307853  4 3.738108e-08 1.817332e-06
9337 ENSG00000196951.12  34.181971  2 3.779892e-08 1.826160e-06
2441 ENSG00000144677.15  30.184504  1 3.928357e-08 1.886099e-06
3389 ENSG00000148187.18  40.174935  4 3.982429e-08 1.900258e-06
9804  ENSG00000280739.4  37.056423  3 4.476622e-08 2.122962e-06
8578  ENSG00000225953.4  29.774921  1 4.852286e-08 2.287084e-06
2395 ENSG00000143569.19  33.559134  2 5.160913e-08 2.417810e-06
5024 ENSG00000179222.18  29.609283  1 5.285123e-08 2.461084e-06
270  ENSG00000089009.16  29.276099  1 6.276513e-08 2.905236e-06
6323 ENSG00000068831.19  33.093598  2 6.513532e-08 2.997000e-06
4877 ENSG00000156976.17  39.042277  4 6.827766e-08 3.122996e-06
6210 ENSG00000085511.20  32.982841  2 6.884414e-08 3.130384e-06
8700  ENSG00000228624.8  35.872102  3 7.969431e-08 3.602556e-06
3936 ENSG00000166377.21  32.629798  2 8.213522e-08 3.691310e-06
2729 ENSG00000152582.14  28.635998  1 8.734325e-08 3.902678e-06
4627 ENSG00000166938.13  32.463282  2 8.926638e-08 3.965684e-06
3449 ENSG00000166169.17  38.460580  4 9.003126e-08 3.976809e-06
2977 ENSG00000127603.32  38.447548  4 9.059062e-08 3.978781e-06
6875 ENSG00000111237.19  35.518433  3 9.466418e-08 4.134204e-06
3443 ENSG00000166130.15  32.250618  2 9.928128e-08 4.311485e-06
6401 ENSG00000135951.16  43.031465  6 1.149831e-07 4.965473e-06
2521 ENSG00000112531.17  31.767052  2 1.264364e-07 5.429742e-06
3110 ENSG00000161835.11  31.638544  2 1.348272e-07 5.758090e-06
9017 ENSG00000183666.18  40.140494  5 1.399046e-07 5.942102e-06
6602  ENSG00000244274.9  34.670277  3 1.430172e-07 6.041109e-06
6654 ENSG00000138757.15  31.312271  2 1.587182e-07 6.667891e-06
5588 ENSG00000075420.13  31.228435  2 1.655128e-07 6.915750e-06
8943 ENSG00000137601.18  34.344163  3 1.675948e-07 6.965096e-06
3508 ENSG00000166847.10  31.168184  2 1.705748e-07 7.051032e-06
6184 ENSG00000116698.22  34.089386  3 1.896946e-07 7.799677e-06
6807 ENSG00000155974.13  30.894461  2 1.955929e-07 7.999644e-06
5105  ENSG00000184014.9  33.933080  3 2.046692e-07 8.326803e-06
6400 ENSG00000107518.18  30.779983  2 2.071150e-07 8.382194e-06
9881  ENSG00000288663.1  30.534060  2 2.342141e-07 9.382836e-06
6214 ENSG00000100241.22  36.445810  4 2.342674e-07 9.382836e-06
3388 ENSG00000165156.15  30.268887  2 2.674204e-07 1.065546e-05
6584 ENSG00000173209.23  30.225886  2 2.732324e-07 1.083121e-05
862  ENSG00000108848.16  30.179980  2 2.795764e-07 1.102615e-05
3555 ENSG00000197380.11  29.965810  2 3.111767e-07 1.221013e-05
5862 ENSG00000068366.21  33.008643  3 3.207182e-07 1.252097e-05
3073 ENSG00000160917.15  26.098849  1 3.243773e-07 1.260018e-05
4736 ENSG00000168010.11  32.751862  3 3.633136e-07 1.404207e-05
1706 ENSG00000109046.15  29.436332  2 4.054916e-07 1.559428e-05
2108 ENSG00000124920.14  32.423979  3 4.260091e-07 1.630223e-05
6402 ENSG00000133961.21  32.340787  3 4.435653e-07 1.684884e-05
3958 ENSG00000217128.13  25.490127  1 4.446525e-07 1.684884e-05
3983 ENSG00000174099.12  25.463394  1 4.508566e-07 1.700059e-05
7160 ENSG00000160710.18  25.453767  1 4.531119e-07 1.700270e-05
3154 ENSG00000122417.15  35.020900  4 4.599654e-07 1.717649e-05
5100 ENSG00000174010.10  29.124433  2 4.739251e-07 1.761270e-05
3873 ENSG00000141524.17  28.970323  2 5.118873e-07 1.893248e-05
872  ENSG00000114354.15  28.850974  2 5.433637e-07 1.990988e-05
9653 ENSG00000167680.17  28.850601  2 5.434650e-07 1.990988e-05
8817 ENSG00000133657.17  28.707677  2 5.837234e-07 2.128388e-05
7903 ENSG00000205572.10  28.680617  2 5.916748e-07 2.147252e-05
8347 ENSG00000221978.13  31.658224  3 6.177428e-07 2.231379e-05
1031 ENSG00000127511.10  24.796045  1 6.372811e-07 2.282648e-05
838  ENSG00000119950.21  36.863677  5 6.378420e-07 2.282648e-05
695  ENSG00000112715.26  36.443569  5 7.742253e-07 2.757955e-05
6252 ENSG00000072518.22  30.973588  3 8.610027e-07 3.053005e-05
4534 ENSG00000140538.16  27.872091  2 8.864462e-07 3.128872e-05
2700 ENSG00000109670.16  33.549476  4 9.217794e-07 3.238798e-05
3057 ENSG00000160685.14  27.784251  2 9.262463e-07 3.239767e-05
2830 ENSG00000155100.11  27.518268  2 1.057996e-06 3.683924e-05
5979 ENSG00000107758.16  30.323887  3 1.179659e-06 4.089133e-05
3848  ENSG00000124134.9  23.486317  1 1.258053e-06 4.333608e-05
3930 ENSG00000120549.18  23.478747  1 1.263013e-06 4.333608e-05
3194 ENSG00000163249.13  27.157708  2 1.267006e-06 4.333608e-05
8334  ENSG00000215375.6  32.819935  4 1.300288e-06 4.427853e-05
9251 ENSG00000245694.11  30.031519  3 1.359148e-06 4.607990e-05
4181 ENSG00000164114.19  29.985995  3 1.389450e-06 4.690152e-05
5537 ENSG00000101236.17  23.254276  1 1.419345e-06 4.770234e-05
5186 ENSG00000184588.18  23.208381  1 1.453624e-06 4.864293e-05
5612 ENSG00000169764.16  23.156333  1 1.493506e-06 4.976206e-05
4771 ENSG00000137411.19  29.803794  3 1.517625e-06 5.034869e-05
178  ENSG00000060642.12  32.421428  4 1.568827e-06 5.182494e-05
4879 ENSG00000108515.18  29.626329  3 1.653802e-06 5.439952e-05
6650 ENSG00000182841.13  29.591340  3 1.682056e-06 5.509445e-05
2290 ENSG00000141068.15  26.445227  2 1.809223e-06 5.900967e-05
8228  ENSG00000250151.9  29.365540  3 1.876340e-06 6.091132e-05
6222 ENSG00000146833.16  22.710574  1 1.883287e-06 6.091132e-05
3650 ENSG00000168522.13  26.278989  2 1.966030e-06 6.332253e-05
3575 ENSG00000167548.18  31.789149  4 2.112620e-06 6.776162e-05
5528 ENSG00000130985.17  22.479683  1 2.123781e-06 6.783813e-05
4253 ENSG00000112763.17  29.098190  3 2.135520e-06 6.793238e-05
2932 ENSG00000148219.18  31.650957  4 2.254496e-06 7.142317e-05
210  ENSG00000067840.13  25.911071  2 2.363102e-06 7.455828e-05
4031  ENSG00000173905.9  22.226227  1 2.423408e-06 7.615017e-05
8326 ENSG00000185201.18  25.840696  2 2.447734e-06 7.660317e-05
7283 ENSG00000067208.16  25.831023  2 2.459601e-06 7.666419e-05
827   ENSG00000119640.9  28.702113  3 2.586556e-06 8.014894e-05
4614 ENSG00000111679.17  25.726054  2 2.592139e-06 8.014894e-05
8391 ENSG00000105889.16  31.269754  4 2.696986e-06 8.305858e-05
9143  ENSG00000269743.3  21.921488  1 2.840356e-06 8.712678e-05
1597 ENSG00000111450.14  21.905985  1 2.863395e-06 8.748634e-05
382  ENSG00000088833.18  25.445270  2 2.982838e-06 9.077693e-05
1425 ENSG00000136448.13  28.370202  3 3.036900e-06 9.205975e-05
8028 ENSG00000087152.16  25.368220  2 3.099996e-06 9.360535e-05
7200 ENSG00000151923.18  28.278933  3 3.173909e-06 9.546427e-05
4980 ENSG00000100614.18  28.234791  3 3.242367e-06 9.714534e-05
2554 ENSG00000147601.15  25.068980  2 3.600312e-06 1.074533e-04
6155 ENSG00000214063.12  27.995165  3 3.640533e-06 1.082359e-04
3216 ENSG00000163513.19  25.005233  2 3.716914e-06 1.100833e-04
6591 ENSG00000122126.18  21.387398  1 3.752294e-06 1.107070e-04
1314 ENSG00000134046.12  24.880491  2 3.956125e-06 1.162770e-04
4100 ENSG00000125462.19  30.377729  4 4.099929e-06 1.200472e-04
1159 ENSG00000203485.14  30.354095  4 4.145638e-06 1.209275e-04
4950 ENSG00000105443.16  27.697243  3 4.204226e-06 1.221754e-04
7526 ENSG00000118707.11  21.073542  1 4.419888e-06 1.279616e-04
7524 ENSG00000119397.19  24.602696  2 4.545613e-06 1.311104e-04
6019 ENSG00000057663.16  24.574631  2 4.609849e-06 1.324689e-04
6523 ENSG00000008838.21  24.517429  2 4.743599e-06 1.358075e-04
1440 ENSG00000136717.15  27.420074  3 4.806534e-06 1.371015e-04
2783 ENSG00000153904.21  20.886055  1 4.874301e-06 1.385233e-04
6164 ENSG00000136754.18  24.357298  2 5.139016e-06 1.455113e-04
9602  ENSG00000262001.2  24.221155  2 5.501018e-06 1.551930e-04
2984 ENSG00000159079.19  27.099982  3 5.609943e-06 1.574348e-04
4698 ENSG00000177119.17  20.613032  1 5.621217e-06 1.574348e-04
1600 ENSG00000038532.16  24.157481  2 5.678972e-06 1.584782e-04
6421 ENSG00000135316.19  32.007055  5 5.922179e-06 1.646707e-04
276  ENSG00000090006.18  29.580131  4 5.958543e-06 1.650879e-04
3251 ENSG00000163728.11  23.955144  2 6.283571e-06 1.734714e-04
401   ENSG00000101846.9  23.944863  2 6.315955e-06 1.735227e-04
8790 ENSG00000170381.14  23.940318  2 6.330325e-06 1.735227e-04
5162 ENSG00000101361.17  20.352943  1 6.439398e-06 1.758889e-04
1346 ENSG00000092421.17  20.311714  1 6.579654e-06 1.790871e-04
1133 ENSG00000100364.19  23.815825  2 6.736886e-06 1.827233e-04
5401 ENSG00000197928.11  23.787858  2 6.831754e-06 1.846484e-04
8205 ENSG00000100167.21  23.622294  2 7.421369e-06 1.998856e-04
8720 ENSG00000153363.14  28.996610  4 7.829794e-06 2.101539e-04
9301 ENSG00000249859.13  33.602009  6 8.028674e-06 2.147462e-04
7615 ENSG00000168477.19  28.858330  4 8.352868e-06 2.226471e-04
7993 ENSG00000175161.14  23.334589  2 8.569555e-06 2.276380e-04
8983  ENSG00000272168.9  33.407287  6 8.753436e-06 2.317262e-04
128  ENSG00000010219.14  28.736004  4 8.844503e-06 2.330344e-04
2185 ENSG00000087470.19  23.267218  2 8.863146e-06 2.330344e-04
3062 ENSG00000160781.17  33.356734  6 8.951976e-06 2.345721e-04
9329  ENSG00000213777.5  23.136490  2 9.461830e-06 2.470944e-04
1998 ENSG00000108306.13  22.954075  2 1.036540e-05 2.697795e-04
6760 ENSG00000196235.14  22.880396  2 1.075437e-05 2.789641e-04
1273 ENSG00000132768.14  22.813053  2 1.112266e-05 2.875523e-04
6737 ENSG00000171204.13  25.660595  3 1.123250e-05 2.894242e-04
2025  ENSG00000105088.9  22.757281  2 1.143719e-05 2.937191e-04
1018 ENSG00000126787.13  19.217652  1 1.166299e-05 2.985262e-04
245  ENSG00000079156.17  28.113378  4 1.183006e-05 3.018032e-04
973  ENSG00000125637.16  22.663603  2 1.198564e-05 3.047664e-04
1225 ENSG00000131759.18  22.639618  2 1.213024e-05 3.074319e-04
5992 ENSG00000158321.18  28.051576  4 1.217629e-05 3.075905e-04
4645 ENSG00000141447.19  22.584115  2 1.247159e-05 3.140239e-04
6526 ENSG00000087266.17  22.575039  2 1.252831e-05 3.144281e-04
4179 ENSG00000102786.15  22.556269  2 1.264644e-05 3.159151e-04
7829 ENSG00000177189.14  19.059687  1 1.266930e-05 3.159151e-04
6987 ENSG00000198839.10  19.053116  1 1.271300e-05 3.159856e-04
738  ENSG00000114993.17  22.488535  2 1.308208e-05 3.241169e-04
6180 ENSG00000130255.13  22.460371  2 1.326760e-05 3.276631e-04
1798 ENSG00000120616.16  18.953935  1 1.339128e-05 3.296644e-04
1016 ENSG00000126759.14  22.337818  2 1.410602e-05 3.461572e-04
3513 ENSG00000166881.10  18.751576  1 1.489003e-05 3.642402e-04
3549 ENSG00000167323.12  18.707571  1 1.523763e-05 3.711384e-04
8078 ENSG00000186017.16  25.023329  3 1.526805e-05 3.711384e-04
6494  ENSG00000234719.9  22.157733  2 1.543510e-05 3.740229e-04
3972 ENSG00000175309.15  24.987361  3 1.553473e-05 3.752609e-04
3347  ENSG00000164615.6  22.100983  2 1.587934e-05 3.823904e-04
6370 ENSG00000197857.15  18.581782  1 1.627686e-05 3.907458e-04
5259 ENSG00000182919.15  27.335990  4 1.699950e-05 4.063985e-04
3979 ENSG00000174628.16  24.795955  3 1.703404e-05 4.063985e-04
8095 ENSG00000164889.15  18.356831  1 1.831611e-05 4.355489e-04
3231 ENSG00000163638.13  21.809741  2 1.836855e-05 4.355489e-04
7521 ENSG00000180198.17  21.744435  2 1.897824e-05 4.486293e-04
1204 ENSG00000131051.24  21.696297  2 1.944057e-05 4.581573e-04
8599 ENSG00000121671.12  18.224989  1 1.962865e-05 4.600637e-04
6369 ENSG00000198208.12  29.367314  5 1.964049e-05 4.600637e-04
179  ENSG00000061273.18  24.440236  3 2.021398e-05 4.720666e-04
8400 ENSG00000164199.18  21.525565  2 2.117303e-05 4.929744e-04
449  ENSG00000103534.17  24.221207  3 2.245961e-05 5.213596e-04
2046 ENSG00000109586.12  17.913976  1 2.311177e-05 5.348922e-04
125  ENSG00000010270.14  21.284245  2 2.388828e-05 5.512132e-04
1493 ENSG00000137841.12  26.510814  4 2.495914e-05 5.742088e-04
64   ENSG00000176092.17  21.182659  2 2.513299e-05 5.764925e-04
618  ENSG00000109944.11  21.170091  2 2.529142e-05 5.784103e-04
671  ENSG00000010810.17  21.161808  2 2.539638e-05 5.790974e-04
157  ENSG00000040608.14  17.706023  1 2.578091e-05 5.861365e-04
4358 ENSG00000172785.18  21.099474  2 2.620037e-05 5.939263e-04
4628 ENSG00000107186.17  26.386437  4 2.644472e-05 5.977125e-04
2135 ENSG00000105865.11  21.047776  2 2.688646e-05 6.059252e-04
7513 ENSG00000204131.10  17.599700  1 2.726314e-05 6.126281e-04
4267 ENSG00000129347.21  20.933759  2 2.846374e-05 6.377528e-04
8054 ENSG00000140104.14  23.716927  3 2.862048e-05 6.391957e-04
9208  ENSG00000245248.8  17.502467  1 2.869352e-05 6.391957e-04
6515 ENSG00000196498.13  17.451935  1 2.946642e-05 6.545272e-04
6330 ENSG00000187391.22  26.067986  4 3.066126e-05 6.791161e-04
7050 ENSG00000143353.12  23.529512  3 3.131705e-05 6.916594e-04
2205 ENSG00000072041.18  20.680683  2 3.230329e-05 7.114087e-04
4790 ENSG00000111641.12  17.249727  1 3.277447e-05 7.183462e-04
6244 ENSG00000132780.17  23.432926  3 3.280417e-05 7.183462e-04
6845 ENSG00000150636.17  23.408209  3 3.319590e-05 7.248709e-04
5322 ENSG00000169756.16  17.187581  1 3.386430e-05 7.373831e-04
5640 ENSG00000095794.20  23.319425  3 3.464187e-05 7.521956e-04
8353 ENSG00000132763.15  17.134714  1 3.482005e-05 7.539466e-04
8500  ENSG00000224032.8  20.482991  2 3.565948e-05 7.699659e-04
4160 ENSG00000178821.13  20.476682  2 3.577215e-05 7.702471e-04
7234 ENSG00000148834.13  17.038246  1 3.663443e-05 7.866226e-04
1719 ENSG00000064651.14  17.009166  1 3.719979e-05 7.961979e-04
3883 ENSG00000172348.16  17.004753  1 3.728637e-05 7.961979e-04
1991 ENSG00000114251.15  16.974054  1 3.789415e-05 8.069472e-04
7251 ENSG00000166272.18  16.959599  1 3.818377e-05 8.108807e-04
803  ENSG00000118473.23  25.515579  4 3.961968e-05 8.384681e-04
7554 ENSG00000096433.11  16.885689  1 3.969978e-05 8.384681e-04
7183 ENSG00000197498.13  20.249398  2 4.007736e-05 8.441361e-04
6209 ENSG00000173267.14  16.838766  1 4.069349e-05 8.540366e-04
7472 ENSG00000185513.17  16.832043  1 4.083789e-05 8.540366e-04
3430  ENSG00000165916.9  20.209795  2 4.087885e-05 8.540366e-04
5224 ENSG00000183250.13  22.952145  3 4.132122e-05 8.609515e-04
650   ENSG00000111348.9  16.777677  1 4.202478e-05 8.732569e-04
5310 ENSG00000058673.17  25.301717  4 4.374838e-05 9.064375e-04
2090 ENSG00000075223.14  16.696749  1 4.385610e-05 9.064375e-04
2943 ENSG00000137834.15  16.644186  1 4.508829e-05 9.294200e-04
7965 ENSG00000104723.21  25.208026  4 4.568922e-05 9.393023e-04
2297 ENSG00000141314.13  16.534299  1 4.777796e-05 9.796382e-04
1872 ENSG00000129810.15  25.089242  4 4.827331e-05 9.871764e-04
3719 ENSG00000169057.24  19.812724  2 4.985648e-05 1.016862e-03
7661 ENSG00000204498.11  19.705489  2 5.260262e-05 1.070048e-03
2056 ENSG00000113319.13  19.693359  2 5.292263e-05 1.073732e-03
1228 ENSG00000089280.19  22.399648  3 5.386040e-05 1.089898e-03
1559 ENSG00000109790.18  16.282377  1 5.456912e-05 1.099601e-03
16   ENSG00000140750.17  19.630059  2 5.462441e-05 1.099601e-03
5914 ENSG00000125848.10  16.230981  1 5.606963e-05 1.125762e-03
6149 ENSG00000065534.20  22.310068  3 5.622386e-05 1.125934e-03
668  ENSG00000111790.14  22.286973  3 5.684974e-05 1.135526e-03
4726 ENSG00000177302.15  19.538959  2 5.717012e-05 1.138982e-03
3369 ENSG00000164919.11  16.185649  1 5.742754e-05 1.141169e-03
5146 ENSG00000184640.20  22.259677  3 5.759846e-05 1.141631e-03
5983 ENSG00000124104.19  22.128620  3 6.133234e-05 1.212529e-03
4128 ENSG00000149187.19  19.374713  2 6.206324e-05 1.221053e-03
7443 ENSG00000241343.10  22.103355  3 6.207941e-05 1.221053e-03
1548 ENSG00000069493.15  22.071619  3 6.303068e-05 1.236617e-03
2752 ENSG00000183889.12  22.033728  3 6.418549e-05 1.256086e-03
9266  ENSG00000250802.7  24.437217  4 6.526967e-05 1.274077e-03
3823 ENSG00000112419.15  15.919676  1 6.608811e-05 1.286804e-03
136  ENSG00000012061.16  21.967018  3 6.627005e-05 1.287104e-03
1272 ENSG00000132749.11  19.203814  2 6.759968e-05 1.309638e-03
4276 ENSG00000081803.17  19.141440  2 6.974115e-05 1.347748e-03
6879 ENSG00000134884.15  15.770552  1 7.150686e-05 1.378424e-03
3092 ENSG00000161265.15  28.604281  6 7.227440e-05 1.389754e-03
1377 ENSG00000135636.15  19.057730  2 7.272210e-05 1.394893e-03
3991 ENSG00000164305.19  15.714527  1 7.365631e-05 1.409315e-03
4545 ENSG00000138835.22  21.672918  3 7.629403e-05 1.456180e-03
8489 ENSG00000163882.10  24.085026  4 7.680055e-05 1.462237e-03
8857  ENSG00000256646.8  18.893023  2 7.896457e-05 1.499745e-03
6337 ENSG00000170456.16  15.568963  1 7.954975e-05 1.507156e-03
4948 ENSG00000137473.19  15.558157  1 8.000572e-05 1.512088e-03
2550 ENSG00000147526.20  18.792673  2 8.302767e-05 1.565375e-03
6424 ENSG00000100938.19  21.463344  3 8.434545e-05 1.586351e-03
60    ENSG00000265992.1  15.438476  1 8.523509e-05 1.599192e-03
3824 ENSG00000121289.18  21.433321  3 8.556619e-05 1.601517e-03
1759 ENSG00000035862.12  15.408456  1 8.659988e-05 1.616950e-03
1500 ENSG00000137942.18  15.402739  1 8.686231e-05 1.617941e-03
8283 ENSG00000104885.19  15.298171  1 9.180533e-05 1.705902e-03
7629 ENSG00000076053.12  21.267981  3 9.261104e-05 1.716747e-03
1330 ENSG00000134324.12  15.228031  1 9.527865e-05 1.761971e-03
9044  ENSG00000279170.3  23.612227  4 9.551848e-05 1.762191e-03
4885  ENSG00000213928.9  21.187013  3 9.626874e-05 1.767664e-03
3888 ENSG00000172239.14  15.208433  1 9.627253e-05 1.767664e-03
4876 ENSG00000168952.16  18.488089  2 9.668576e-05 1.771045e-03
595  ENSG00000108773.11  15.188967  1 9.727006e-05 1.777536e-03
2626 ENSG00000125991.21  15.123862  1 1.006826e-04 1.833110e-03
1509 ENSG00000138078.16  18.405032  2 1.007855e-04 1.833110e-03
236  ENSG00000064763.12  23.485175  4 1.012784e-04 1.837751e-03
7450 ENSG00000102384.14  18.370455  2 1.025431e-04 1.856342e-03
9626  ENSG00000265479.7  18.336493  2 1.042992e-04 1.883722e-03
7731 ENSG00000149474.15  18.317955  2 1.052705e-04 1.896832e-03
1525 ENSG00000171681.13  20.939541  3 1.083640e-04 1.948032e-03
7687 ENSG00000106772.19  20.932653  3 1.087215e-04 1.949924e-03
2563 ENSG00000148019.14  25.524584  5 1.103183e-04 1.973982e-03
2103 ENSG00000004866.22  18.214575  2 1.108550e-04 1.979005e-03
9735  ENSG00000273136.8  18.204490  2 1.114154e-04 1.984427e-03
3981 ENSG00000174136.13  14.916761  1 1.123603e-04 1.996655e-03
3301  ENSG00000164100.9  14.889556  1 1.139923e-04 2.021011e-03
2969 ENSG00000158604.15  14.867861  1 1.153109e-04 2.039711e-03
2892 ENSG00000156925.12  14.836308  1 1.172562e-04 2.069384e-03
6741 ENSG00000165280.18  14.827566  1 1.178009e-04 2.074263e-03
5638 ENSG00000122565.19  14.822205  1 1.181363e-04 2.075440e-03
9068 ENSG00000149260.18  14.759243  1 1.221473e-04 2.141039e-03
8192 ENSG00000185219.18  14.731705  1 1.239444e-04 2.166503e-03
3774 ENSG00000168958.20  20.654852  3 1.241605e-04 2.166503e-03
6551 ENSG00000160752.15  17.956926  2 1.260965e-04 2.195329e-03
4363  ENSG00000181264.9  17.919146  2 1.285011e-04 2.232166e-03
305  ENSG00000099219.15  17.860424  2 1.323300e-04 2.293521e-03
6927 ENSG00000198925.12  17.847782  2 1.331691e-04 2.302901e-03
3899 ENSG00000170234.13  14.530848  1 1.378832e-04 2.379101e-03
1325 ENSG00000134285.11  20.404099  3 1.399614e-04 2.409580e-03
2057 ENSG00000113318.11  14.479260  1 1.417112e-04 2.434284e-03
7997 ENSG00000156983.17  24.903021  5 1.454713e-04 2.491669e-03
7372 ENSG00000160345.13  14.427023  1 1.456966e-04 2.491669e-03
7968 ENSG00000100150.20  22.672525  4 1.471998e-04 2.511820e-03
6598 ENSG00000116560.11  17.636965  2 1.479727e-04 2.518396e-03
274   ENSG00000249115.9  14.394473  1 1.482368e-04 2.518396e-03
5930 ENSG00000103168.17  17.620955  2 1.491620e-04 2.528558e-03
4157 ENSG00000115677.18  14.377098  1 1.496109e-04 2.529352e-03
4747 ENSG00000177311.12  14.373924  1 1.498633e-04 2.529352e-03
5716 ENSG00000168003.18  17.562897  2 1.535555e-04 2.586021e-03
5080 ENSG00000198040.11  14.315920  1 1.545523e-04 2.597150e-03
9211  ENSG00000245498.7  24.732806  5 1.568973e-04 2.630838e-03
4032 ENSG00000002330.14  14.274407  1 1.579986e-04 2.643569e-03
5556 ENSG00000143702.16  17.479866  2 1.600646e-04 2.672353e-03
6413 ENSG00000133104.14  17.474741  2 1.604753e-04 2.673436e-03
4798 ENSG00000136709.12  14.220842  1 1.625601e-04 2.702343e-03
6199 ENSG00000119139.21  17.442853  2 1.630544e-04 2.704744e-03
2722 ENSG00000152495.11  17.410320  2 1.657285e-04 2.742884e-03
5045 ENSG00000157216.16  17.406282  2 1.660634e-04 2.742884e-03
4818 ENSG00000117335.20  17.387420  2 1.676369e-04 2.762971e-03
3623 ENSG00000085733.16  14.138665  1 1.698172e-04 2.788905e-03
9060  ENSG00000235823.4  19.997661  3 1.699320e-04 2.788905e-03
6621 ENSG00000112200.17  19.978516  3 1.714915e-04 2.808537e-03
2665 ENSG00000151092.18  19.968049  3 1.723502e-04 2.810986e-03
2827 ENSG00000154917.11  14.110615  1 1.723683e-04 2.810986e-03
3246 ENSG00000163704.12  14.097740  1 1.735522e-04 2.824334e-03
7551 ENSG00000158006.14  14.088552  1 1.744020e-04 2.832201e-03
2092 ENSG00000099250.18  19.847244  3 1.825754e-04 2.958717e-03
7851 ENSG00000205726.15  17.168668  2 1.870127e-04 3.024285e-03
6806 ENSG00000146373.17  19.767299  3 1.896719e-04 3.060885e-03
2495 ENSG00000145736.14  19.744955  3 1.917040e-04 3.087233e-03
7284 ENSG00000075826.17  22.066734  4 1.943823e-04 3.123857e-03
3043 ENSG00000160310.19  22.061317  4 1.948656e-04 3.125128e-03
765  ENSG00000115806.13  13.867225  1 1.961902e-04 3.133190e-03
8549  ENSG00000237943.8  19.693166  3 1.964976e-04 3.133190e-03
6217 ENSG00000176700.21  19.692240  3 1.965843e-04 3.133190e-03
7976 ENSG00000155269.12  13.851950  1 1.977914e-04 3.145942e-03
5618 ENSG00000083312.19  17.016255  2 2.018214e-04 3.203448e-03
1366 ENSG00000135424.19  19.584353  3 2.069614e-04 3.278303e-03
4268 ENSG00000081177.19  21.924742  4 2.074531e-04 3.279372e-03
1570 ENSG00000092020.11  16.926688  2 2.110651e-04 3.329660e-03
4443 ENSG00000107957.17  16.890133  2 2.149584e-04 3.384171e-03
6288 ENSG00000157766.19  21.827772  4 2.168768e-04 3.407434e-03
3948 ENSG00000100461.18  16.841412  2 2.202591e-04 3.453555e-03
3108 ENSG00000161813.23  16.832740  2 2.212163e-04 3.455811e-03
4096 ENSG00000154889.17  23.956855  5 2.212971e-04 3.455811e-03
1618 ENSG00000103876.14  16.826286  2 2.219312e-04 3.458726e-03
1303 ENSG00000133812.18  13.627921  1 2.228465e-04 3.464876e-03
9508  ENSG00000259479.6  16.814685  2 2.232223e-04 3.464876e-03
6050 ENSG00000129691.16  13.567275  1 2.301632e-04 3.565455e-03
6284 ENSG00000128191.16  16.748030  2 2.307871e-04 3.567969e-03
3594 ENSG00000167703.15  19.351040  3 2.313043e-04 3.568827e-03
5872 ENSG00000164828.18  23.799716  5 2.372213e-04 3.652830e-03
7583 ENSG00000182667.15  16.681780  2 2.385599e-04 3.666139e-03
4855 ENSG00000070814.22  16.674099  2 2.394778e-04 3.672944e-03
1027 ENSG00000130803.15  13.488843  1 2.399862e-04 3.673452e-03
8161 ENSG00000110031.13  16.645688  2 2.429041e-04 3.710768e-03
2421 ENSG00000144306.15  16.615349  2 2.466169e-04 3.755481e-03
6513 ENSG00000008128.23  16.613843  2 2.468026e-04 3.755481e-03
1080 ENSG00000129255.16  13.430351  1 2.475858e-04 3.759997e-03
547  ENSG00000106477.20  19.182092  3 2.506907e-04 3.798296e-03
3196 ENSG00000152795.18  13.403984  1 2.510904e-04 3.798296e-03
913  ENSG00000123415.16  19.174287  3 2.516245e-04 3.798939e-03
8818  ENSG00000227398.5  16.568910  2 2.524102e-04 3.803374e-03
2070 ENSG00000138802.11  16.557784  2 2.538182e-04 3.817150e-03
2884 ENSG00000156650.14  23.600894  5 2.590015e-04 3.887538e-03
5827 ENSG00000135047.16  19.099418  3 2.607583e-04 3.903690e-03
4723 ENSG00000005436.14  16.501308  2 2.610877e-04 3.903690e-03
1042 ENSG00000127824.15  13.325499  1 2.618212e-04 3.907100e-03
2170 ENSG00000107864.15  16.464060  2 2.659959e-04 3.960522e-03
57   ENSG00000131375.10  13.290845  1 2.667052e-04 3.960522e-03
5337 ENSG00000182718.18  13.285965  1 2.674004e-04 3.960522e-03
7392 ENSG00000160271.16  21.369742  4 2.674505e-04 3.960522e-03
4928 ENSG00000116191.19  13.245435  1 2.732445e-04 4.038586e-03
942  ENSG00000234465.11  18.993045  3 2.743056e-04 4.046532e-03
1935 ENSG00000117298.16  18.966029  3 2.778565e-04 4.091106e-03
2016 ENSG00000080709.16  16.354318  2 2.809991e-04 4.129511e-03
7705 ENSG00000136160.17  18.922519  3 2.836714e-04 4.160873e-03
8059  ENSG00000212123.4  13.132981  1 2.901428e-04 4.247734e-03
4189 ENSG00000130349.10  18.793702  3 3.016069e-04 4.407224e-03
2826 ENSG00000167100.15  18.782062  3 3.032821e-04 4.423341e-03
8842 ENSG00000100888.15  21.085101  4 3.046003e-04 4.434201e-03
9322  ENSG00000281501.1  13.032966  1 3.060554e-04 4.442831e-03
5982 ENSG00000111206.13  18.760960  3 3.063427e-04 4.442831e-03
5039 ENSG00000171606.18  18.705123  3 3.145901e-04 4.553898e-03
6429 ENSG00000196776.17  18.654550  3 3.222505e-04 4.656068e-03
3937 ENSG00000171552.14  23.064719  5 3.280834e-04 4.731501e-03
3531 ENSG00000167085.13  12.826355  1 3.417710e-04 4.919720e-03
6542 ENSG00000105220.17  15.938292  2 3.459744e-04 4.970970e-03
5581 ENSG00000172375.14  18.480807  3 3.500090e-04 5.019610e-03
87    ENSG00000253507.6  15.907010  2 3.514282e-04 5.030630e-03
2596 ENSG00000213593.10  12.754858  1 3.550858e-04 5.073592e-03
2877 ENSG00000156453.14  15.879172  2 3.563539e-04 5.082317e-03
9054 ENSG00000146556.15  18.426562  3 3.591536e-04 5.112812e-03
7770 ENSG00000182220.15  20.712836  4 3.609992e-04 5.129640e-03
5891 ENSG00000055732.13  18.396534  3 3.643174e-04 5.167291e-03
1382 ENSG00000205084.12  22.790199  5 3.702061e-04 5.241197e-03
4308 ENSG00000102984.15  18.348830  3 3.726731e-04 5.266477e-03
9355  ENSG00000253210.3  18.306038  3 3.803303e-04 5.364878e-03
5974 ENSG00000188313.13  18.295055  3 3.823209e-04 5.377957e-03
9828  ENSG00000283196.2  15.736785  2 3.826490e-04 5.377957e-03
6744 ENSG00000008311.16  12.611091  1 3.834646e-04 5.379639e-03
3732 ENSG00000171735.19  18.284937  3 3.841636e-04 5.379683e-03
5353  ENSG00000182057.5  15.719335  2 3.860021e-04 5.395653e-03
6395 ENSG00000197586.13  15.567561  2 4.164348e-04 5.809252e-03
1322 ENSG00000134245.18  15.564399  2 4.170938e-04 5.809252e-03
557  ENSG00000081386.13  12.446401  1 4.187980e-04 5.822497e-03
8640 ENSG00000099810.21  15.549489  2 4.202149e-04 5.831707e-03
2168 ENSG00000051009.11  18.076248  3 4.242064e-04 5.876550e-03
8109 ENSG00000133640.20  15.514937  2 4.275375e-04 5.912102e-03
483  ENSG00000104852.15  15.510071  2 4.285789e-04 5.915920e-03
8774 ENSG00000237441.10  18.022946  3 4.350826e-04 5.994989e-03
6787 ENSG00000169359.16  18.018723  3 4.359560e-04 5.996335e-03
2485 ENSG00000145536.15  15.470085  2 4.372338e-04 6.003228e-03
6904 ENSG00000197879.17  15.440171  2 4.438226e-04 6.082888e-03
1544 ENSG00000101670.12  17.965304  3 4.471566e-04 6.117736e-03
4214 ENSG00000092108.22  12.320628  1 4.479799e-04 6.118171e-03
5250 ENSG00000179915.25  22.344395  5 4.502615e-04 6.138486e-03
6560 ENSG00000118518.17  17.944370  3 4.516237e-04 6.142944e-03
8460  ENSG00000234741.9  15.401405  2 4.525092e-04 6.142944e-03
6732 ENSG00000077458.13  15.399358  2 4.529726e-04 6.142944e-03
2119 ENSG00000114770.17  15.395424  2 4.538645e-04 6.144260e-03
7742 ENSG00000122707.12  12.292162  1 4.548646e-04 6.147034e-03
5412 ENSG00000186594.15  17.904649  3 4.602217e-04 6.208575e-03
7810  ENSG00000288558.2  15.357939  2 4.624511e-04 6.227782e-03
3492 ENSG00000166716.10  12.249793  1 4.653097e-04 6.255381e-03
9896  ENSG00000289527.1  22.240915  5 4.711611e-04 6.323047e-03
6371 ENSG00000122566.22  15.306014  2 4.746147e-04 6.358357e-03
4377 ENSG00000158062.21  22.208706  5 4.778594e-04 6.390749e-03
394  ENSG00000172264.18  12.190216  1 4.804082e-04 6.413740e-03
2959 ENSG00000102024.19  12.176791  1 4.838782e-04 6.448928e-03
2131 ENSG00000071242.12  12.163394  1 4.873660e-04 6.481935e-03
2568 ENSG00000130653.16  15.246545  2 4.889392e-04 6.481935e-03
395  ENSG00000101276.18  20.044821  4 4.893268e-04 6.481935e-03
138  ENSG00000013563.14  17.773819  3 4.897089e-04 6.481935e-03
6531 ENSG00000073921.18  15.230190  2 4.929540e-04 6.513734e-03
1121 ENSG00000117868.18  15.216443  2 4.963539e-04 6.547467e-03
612  ENSG00000109794.14  22.097123  5 5.017997e-04 6.608027e-03
6236 ENSG00000166833.23  15.171388  2 5.076622e-04 6.657960e-03
3666 ENSG00000121940.17  15.169836  2 5.080565e-04 6.657960e-03
4766 ENSG00000109332.20  17.695817  3 5.081755e-04 6.657960e-03
5176 ENSG00000072736.19  15.138215  2 5.161530e-04 6.751037e-03
364  ENSG00000100599.16  15.134716  2 5.170567e-04 6.751433e-03
7911 ENSG00000145740.20  12.046836  1 5.188036e-04 6.753487e-03
8484 ENSG00000212719.14  15.124765  2 5.196359e-04 6.753487e-03
5307 ENSG00000156531.18  17.644981  3 5.205816e-04 6.753487e-03
59   ENSG00000127483.19  15.120640  2 5.207087e-04 6.753487e-03
6695 ENSG00000197448.14  15.090608  2 5.285867e-04 6.844179e-03
6211 ENSG00000197381.17  17.572399  3 5.388182e-04 6.959859e-03
72   ENSG00000124523.17  15.050397  2 5.393215e-04 6.959859e-03
6273 ENSG00000169062.15  17.564199  3 5.409181e-04 6.968828e-03
3916 ENSG00000170266.16  11.945958  1 5.476607e-04 7.043956e-03
4221 ENSG00000175216.15  15.007044  2 5.511399e-04 7.076929e-03
4333 ENSG00000138668.19  14.996010  2 5.541889e-04 7.093395e-03
406  ENSG00000102081.16  19.770588  4 5.542575e-04 7.093395e-03
1653 ENSG00000110911.17  11.906300  1 5.594441e-04 7.133338e-03
9617  ENSG00000266412.6  11.900996  1 5.610395e-04 7.133338e-03
8380 ENSG00000049323.16  14.971002  2 5.611620e-04 7.133338e-03
9095  ENSG00000219626.9  19.741487  4 5.616293e-04 7.133338e-03
4319 ENSG00000166444.19  14.968044  2 5.619926e-04 7.133338e-03
8457 ENSG00000136279.21  14.940660  2 5.697403e-04 7.219824e-03
7572 ENSG00000133216.17  14.935843  2 5.711140e-04 7.225387e-03
6492 ENSG00000196233.14  11.841486  1 5.792558e-04 7.316088e-03
9817  ENSG00000279765.3  11.838530  1 5.801762e-04 7.316088e-03
4226 ENSG00000123405.14  14.893315  2 5.833884e-04 7.344613e-03
6558 ENSG00000196531.14  14.852213  2 5.955017e-04 7.484923e-03
6632 ENSG00000197563.11  14.844123  2 5.979152e-04 7.503059e-03
5548 ENSG00000131748.16  17.335114  3 6.029857e-04 7.554424e-03
9020  ENSG00000237638.3  11.758608  1 6.056250e-04 7.575212e-03
830  ENSG00000119673.16  14.769015  2 6.207964e-04 7.752433e-03
3201 ENSG00000163374.20  19.495429  4 6.279681e-04 7.829344e-03
7331 ENSG00000152763.17  14.735489  2 6.312905e-04 7.858093e-03
4002 ENSG00000172965.17  19.474263  4 6.340243e-04 7.872969e-03
1660 ENSG00000085415.16  11.669900  1 6.351944e-04 7.872969e-03
272  ENSG00000089063.15  11.668884  1 6.355411e-04 7.872969e-03
3998 ENSG00000048649.14  14.702090  2 6.419214e-04 7.927754e-03
7045 ENSG00000143756.12  11.649517  1 6.421920e-04 7.927754e-03
8152 ENSG00000198720.13  11.647061  1 6.430403e-04 7.927754e-03
5557 ENSG00000157823.17  14.677039  2 6.500123e-04 7.995801e-03
5286 ENSG00000182541.18  14.675143  2 6.506286e-04 7.995801e-03
5643 ENSG00000076928.18  14.629363  2 6.656934e-04 8.167953e-03
9666  ENSG00000197291.9  17.092547  3 6.764336e-04 8.286579e-03
9763  ENSG00000276043.5  14.585881  2 6.803245e-04 8.321057e-03
6491 ENSG00000204681.11  14.582337  2 6.815311e-04 8.322647e-03
2966 ENSG00000184154.16  23.362555  6 6.837131e-04 8.334169e-03
4092 ENSG00000003402.21  17.067116  3 6.846309e-04 8.334169e-03
6388 ENSG00000048740.19  17.052334  3 6.894412e-04 8.379529e-03
5264 ENSG00000183032.12  11.511416  1 6.917005e-04 8.393791e-03
9101 ENSG00000204934.10  11.498752  1 6.964293e-04 8.437928e-03
5200 ENSG00000162614.19  14.530112  2 6.995623e-04 8.462623e-03
8173 ENSG00000168175.15  11.484901  1 7.016388e-04 8.474481e-03
5747  ENSG00000189136.9  14.519128  2 7.034145e-04 8.482675e-03
6462 ENSG00000187239.17  14.499839  2 7.102316e-04 8.545039e-03
5751 ENSG00000165246.15  16.985709  3 7.115415e-04 8.545039e-03
2478  ENSG00000145375.9  14.495140  2 7.119023e-04 8.545039e-03
2953 ENSG00000158186.13  11.431903  1 7.219372e-04 8.652054e-03
4756  ENSG00000181291.8  11.421825  1 7.258635e-04 8.685642e-03
9478  ENSG00000257621.9  14.432832  2 7.344299e-04 8.762783e-03
1654 ENSG00000050426.16  19.149355  4 7.345774e-04 8.762783e-03
1347 ENSG00000134982.17  11.361083  1 7.499909e-04 8.932865e-03
5446 ENSG00000109184.15  14.384924  2 7.522350e-04 8.944066e-03
8202 ENSG00000187735.15  14.382239  2 7.532454e-04 8.944066e-03
1649 ENSG00000119707.14  14.372325  2 7.569884e-04 8.974724e-03
5136 ENSG00000182511.12  11.338039  1 7.593545e-04 8.988990e-03
4437 ENSG00000114779.20  14.351806  2 7.647948e-04 9.031488e-03
6720 ENSG00000198265.12  11.323602  1 7.652813e-04 9.031488e-03
3881 ENSG00000144354.14  14.345962  2 7.670327e-04 9.038358e-03
3491  ENSG00000123575.9  11.305654  1 7.727141e-04 9.091446e-03
3831 ENSG00000172059.11  11.287255  1 7.804098e-04 9.168036e-03
1628  ENSG00000138593.9  11.274724  1 7.856952e-04 9.216121e-03
44   ENSG00000101191.17  18.992594  4 7.885816e-04 9.235963e-03
4882 ENSG00000174720.17  14.286732  2 7.900881e-04 9.239609e-03
7921 ENSG00000100416.15  11.259847  1 7.920173e-04 9.248177e-03
1418 ENSG00000136280.17  16.738183  3 7.999927e-04 9.327215e-03
4201 ENSG00000174796.12  11.224502  1 8.072442e-04 9.397587e-03
2041  ENSG00000114107.9  14.233869  2 8.112498e-04 9.430016e-03
9154 ENSG00000182796.15  18.897797  4 8.231255e-04 9.553694e-03
9265  ENSG00000250284.3  14.196919  2 8.263769e-04 9.577052e-03
329  ENSG00000100105.18  14.180274  2 8.332831e-04 9.642632e-03
9267 ENSG00000188848.17  11.144411  1 8.428524e-04 9.738788e-03
6910 ENSG00000132698.15  14.109327  2 8.633733e-04 9.961008e-03
1866 ENSG00000094975.14  14.079211  2 8.764722e-04 1.008872e-02
8404 ENSG00000185340.15  16.543771  3 8.770527e-04 1.008872e-02
6114 ENSG00000181852.18  16.529821  3 8.828575e-04 1.014040e-02
7462 ENSG00000204084.13  11.042706  1 8.903681e-04 1.021149e-02
6930 ENSG00000131778.20  11.025347  1 8.987445e-04 1.028491e-02
4644 ENSG00000180398.13  11.023011  1 8.998776e-04 1.028491e-02
8503 ENSG00000176124.15  20.755835  5 9.007612e-04 1.028491e-02
2694 ENSG00000151806.14  10.993271  1 9.144328e-04 1.042561e-02
6906 ENSG00000158691.15  13.988241  2 9.172592e-04 1.044244e-02
1896 ENSG00000081320.11  10.967328  1 9.273235e-04 1.054149e-02
5549 ENSG00000155506.19  13.957640  2 9.314018e-04 1.057230e-02
5928 ENSG00000073712.15  13.953624  2 9.332736e-04 1.057801e-02
4578 ENSG00000180769.10  16.401919  3 9.378908e-04 1.061478e-02
1241 ENSG00000132205.11  10.937644  1 9.422989e-04 1.064309e-02
2063 ENSG00000039560.14  10.934530  1 9.438840e-04 1.064309e-02
7782 ENSG00000138050.15  13.929661  2 9.445230e-04 1.064309e-02
9110  ENSG00000267272.5  13.920078  2 9.490596e-04 1.067865e-02
886  ENSG00000122218.16  20.614620  5 9.577101e-04 1.076032e-02
6673 ENSG00000100296.14  16.301627  3 9.834164e-04 1.103310e-02
2588  ENSG00000148948.8  13.843614  2 9.860464e-04 1.104658e-02
6043 ENSG00000162390.18  13.801782  2 1.006888e-03 1.126374e-02
3045 ENSG00000188171.17  10.809667  1 1.009714e-03 1.127904e-02
3195 ENSG00000163281.12  13.789770  2 1.012953e-03 1.128312e-02
4072 ENSG00000173915.16  10.803654  1 1.012999e-03 1.128312e-02
8370 ENSG00000138081.22  13.784823  2 1.015462e-03 1.129427e-02
8475  ENSG00000283154.3  13.780588  2 1.017615e-03 1.130196e-02
4553 ENSG00000128536.16  20.467666  5 1.020737e-03 1.132037e-02
6588 ENSG00000162374.18  16.199431  3 1.032064e-03 1.142959e-02
4391  ENSG00000177738.5  16.186655  3 1.038312e-03 1.148233e-02
4243 ENSG00000072195.15  20.417718  5 1.043075e-03 1.151853e-02
1289 ENSG00000133315.12  10.714458  1 1.063016e-03 1.172199e-02
8010 ENSG00000138756.19  10.701209  1 1.070656e-03 1.178941e-02
3727 ENSG00000170634.13  16.086552  3 1.088579e-03 1.196972e-02
8071 ENSG00000177614.11  10.646444  1 1.102828e-03 1.209685e-02
3541 ENSG00000167191.12  13.618953  2 1.103270e-03 1.209685e-02
8567  ENSG00000234773.8  10.641297  1 1.105901e-03 1.210852e-02
360  ENSG00000100528.12  18.240162  4 1.107601e-03 1.210998e-02
8365 ENSG00000186951.17  10.632089  1 1.111421e-03 1.213458e-02
7809 ENSG00000232859.10  13.600418  2 1.113543e-03 1.214060e-02
4986 ENSG00000128699.14  18.222508  4 1.116446e-03 1.215511e-02
1248 ENSG00000132321.17  13.590993  2 1.118802e-03 1.216363e-02
4731 ENSG00000010244.19  13.545654  2 1.144455e-03 1.242505e-02
561  ENSG00000106692.15  13.536909  2 1.149470e-03 1.245117e-02
1926 ENSG00000082258.13  13.535844  2 1.150082e-03 1.245117e-02
3167 ENSG00000162931.12  15.941923  3 1.165501e-03 1.260045e-02
4741 ENSG00000013441.17  15.905633  3 1.185635e-03 1.280022e-02
8909 ENSG00000169855.21  13.467438  2 1.190099e-03 1.283049e-02
2965 ENSG00000005187.12  13.442552  2 1.205000e-03 1.296175e-02
8414 ENSG00000064547.14  10.481701  1 1.205627e-03 1.296175e-02
1309 ENSG00000133997.12  13.438543  2 1.207418e-03 1.296297e-02
9755  ENSG00000274265.5  10.456167  1 1.222407e-03 1.310569e-02
3819 ENSG00000187741.15  13.404573  2 1.228101e-03 1.314850e-02
1298 ENSG00000133703.14  10.429009  1 1.240513e-03 1.326035e-02
7447 ENSG00000024048.11  10.426686  1 1.242074e-03 1.326035e-02
4224 ENSG00000205560.13  13.379338  2 1.243694e-03 1.326035e-02
1487 ENSG00000137807.16  13.375092  2 1.246337e-03 1.327023e-02
9618 ENSG00000154217.16  13.369027  2 1.250123e-03 1.329223e-02
1672 ENSG00000055609.21  15.782040  3 1.256829e-03 1.334518e-02
1538 ENSG00000118600.13  13.346623  2 1.264205e-03 1.340508e-02
8424 ENSG00000071189.21  15.766319  3 1.266185e-03 1.340768e-02
2569 ENSG00000148396.19  15.760911  3 1.269419e-03 1.342354e-02
3185 ENSG00000163075.13  15.745654  3 1.278587e-03 1.348995e-02
1150  ENSG00000130035.9  13.323057  2 1.279189e-03 1.348995e-02
8081 ENSG00000141526.18  10.368631  1 1.281746e-03 1.349849e-02
3630 ENSG00000171016.13  13.265233  2 1.316713e-03 1.384788e-02
2532 ENSG00000146966.13  15.668267  3 1.326112e-03 1.392778e-02
2069 ENSG00000138798.13  15.664054  3 1.328749e-03 1.393654e-02
9607  ENSG00000284634.1  15.640628  3 1.343508e-03 1.407224e-02
676  ENSG00000112062.11  10.271943  1 1.350685e-03 1.412827e-02
7547 ENSG00000137288.10  13.193518  2 1.364784e-03 1.425646e-02
7696 ENSG00000105357.20  10.247158  1 1.368954e-03 1.427764e-02
6928 ENSG00000170776.22  10.245068  1 1.370505e-03 1.427764e-02
4752 ENSG00000175764.17  13.170788  2 1.380383e-03 1.436119e-02
6953 ENSG00000198771.11  10.212252  1 1.395107e-03 1.449486e-02
3743 ENSG00000169621.10  10.204486  1 1.400995e-03 1.453650e-02
5035  ENSG00000179046.9  13.137920  2 1.403256e-03 1.454044e-02
2701 ENSG00000144445.17  15.542796  3 1.406921e-03 1.455890e-02
3814  ENSG00000169217.9  10.192713  1 1.409967e-03 1.457092e-02
3768 ENSG00000186416.18  13.105878  2 1.425918e-03 1.471609e-02
6474 ENSG00000182534.14  13.096345  2 1.432731e-03 1.476668e-02
2267 ENSG00000140557.12  13.077786  2 1.446088e-03 1.488450e-02
235  ENSG00000065883.17  15.472290  3 1.454455e-03 1.495071e-02
5550 ENSG00000070476.15  15.439090  3 1.477387e-03 1.516627e-02
1046 ENSG00000127863.16  10.090790  1 1.490122e-03 1.527672e-02
5981 ENSG00000188735.13  10.076239  1 1.501936e-03 1.536712e-02
1868 ENSG00000116353.16  15.402725  3 1.502916e-03 1.536712e-02
8544 ENSG00000177640.16  10.065647  1 1.510595e-03 1.542523e-02
2465 ENSG00000145087.13  10.056901  1 1.517783e-03 1.547818e-02
2542 ENSG00000125351.13  10.038304  1 1.533183e-03 1.561463e-02
1086 ENSG00000100968.14  19.503236  5 1.548350e-03 1.574835e-02
7006 ENSG00000164038.16  15.263185  3 1.605008e-03 1.630317e-02
7566 ENSG00000112514.18  15.239636  3 1.622903e-03 1.646331e-02
6485 ENSG00000197321.16  12.843461  2 1.625840e-03 1.647149e-02
3432  ENSG00000165943.5   9.922695  1 1.632531e-03 1.651763e-02
666  ENSG00000111725.11  12.822148  2 1.643259e-03 1.660443e-02
7658 ENSG00000134900.12  15.192067  3 1.659657e-03 1.674824e-02
4629 ENSG00000116212.15   9.887100  1 1.664415e-03 1.677435e-02
1282 ENSG00000141219.16  15.179437  3 1.669554e-03 1.680423e-02
3670 ENSG00000130779.22  17.280458  4 1.704840e-03 1.713650e-02
7582 ENSG00000108094.17  17.277633  4 1.706999e-03 1.713650e-02
6354 ENSG00000197859.11   9.832906  1 1.714173e-03 1.718620e-02
3009 ENSG00000140848.17  12.734959  2 1.716481e-03 1.718704e-02
4762  ENSG00000185015.8   9.814262  1 1.731638e-03 1.731638e-02
3495 ENSG00000166750.10   9.795307  1 1.749578e-03 1.747318e-02
979  ENSG00000125744.12  15.076381  3 1.752526e-03 1.748003e-02
8322 ENSG00000008513.16   9.780423  1 1.763798e-03 1.754880e-02
301  ENSG00000096654.16  12.678868  2 1.765301e-03 1.754880e-02
6831 ENSG00000137486.17   9.777108  1 1.766980e-03 1.754880e-02
3995 ENSG00000138138.14  12.674867  2 1.768836e-03 1.754880e-02
1552 ENSG00000064692.20  15.054368  3 1.770772e-03 1.754880e-02
6203 ENSG00000157450.16  12.661364  2 1.780819e-03 1.762578e-02
6499 ENSG00000019144.20  17.172719  4 1.789143e-03 1.768552e-02
6579 ENSG00000100151.16  12.637486  2 1.802208e-03 1.779191e-02
8519 ENSG00000206337.12   9.735052  1 1.807869e-03 1.782503e-02
5804 ENSG00000001631.17  15.004319  3 1.812961e-03 1.785247e-02
6091 ENSG00000127616.20  14.977418  3 1.836049e-03 1.805682e-02
9089 ENSG00000125675.20  14.961839  3 1.849552e-03 1.814503e-02
9300  ENSG00000249395.4  12.585449  2 1.849713e-03 1.814503e-02
6520 ENSG00000145907.16  12.575017  2 1.859387e-03 1.819688e-02
7173 ENSG00000188643.11  12.573010  2 1.861253e-03 1.819688e-02
8873  ENSG00000235437.9  12.572143  2 1.862061e-03 1.819688e-02
4503 ENSG00000147548.17   9.678180  1 1.864692e-03 1.819958e-02
7239  ENSG00000146242.9   9.664597  1 1.878530e-03 1.831152e-02
6348 ENSG00000197548.13  14.919257  3 1.886966e-03 1.835036e-02
2952 ENSG00000158169.13   9.656077  1 1.887262e-03 1.835036e-02
350  ENSG00000239900.14  12.537981  2 1.894140e-03 1.837719e-02
4863 ENSG00000103051.20   9.648777  1 1.894777e-03 1.837719e-02
4111 ENSG00000214021.17  12.533160  2 1.898711e-03 1.839228e-02
5964 ENSG00000135540.12   9.618994  1 1.925752e-03 1.863087e-02
5204 ENSG00000182054.10  12.493225  2 1.937005e-03 1.871631e-02
5758  ENSG00000180008.9   9.600736  1 1.944994e-03 1.877004e-02
2255 ENSG00000140416.23   9.589854  1 1.956555e-03 1.885807e-02
3123 ENSG00000005513.10   9.582389  1 1.964526e-03 1.891132e-02
4712 ENSG00000153071.15   9.579927  1 1.967163e-03 1.891314e-02
3752 ENSG00000157985.19  12.452946  2 1.976411e-03 1.895522e-02
2451 ENSG00000144840.10  14.820722  3 1.976444e-03 1.895522e-02
141  ENSG00000017797.13   9.543866  1 2.006187e-03 1.921664e-02
7022 ENSG00000160691.19  14.776044  3 2.018390e-03 1.930959e-02
6268 ENSG00000122756.15  12.407514  2 2.021820e-03 1.931850e-02
5570 ENSG00000181577.16  12.396105  2 2.033387e-03 1.938135e-02
7241 ENSG00000121931.16   9.518168  1 2.034476e-03 1.938135e-02
6383 ENSG00000004455.17  16.883946  4 2.035919e-03 1.938135e-02
5543 ENSG00000140382.15   9.510384  1 2.043124e-03 1.942601e-02
8711 ENSG00000233723.10  14.731802  3 2.060796e-03 1.956997e-02
7078 ENSG00000112031.16  12.358844  2 2.071625e-03 1.964867e-02
8912 ENSG00000188828.13   9.456182  1 2.104386e-03 1.993493e-02
2705  ENSG00000123066.9  12.290813  2 2.143304e-03 2.027875e-02
9210  ENSG00000246985.8  16.761505  4 2.150419e-03 2.032120e-02
1915 ENSG00000077232.19  12.274063  2 2.161330e-03 2.039212e-02
9299 ENSG00000001084.13  14.628582  3 2.163200e-03 2.039212e-02
3456 ENSG00000166257.10  14.598497  3 2.193986e-03 2.065714e-02
5298 ENSG00000065357.20   9.350595  1 2.229131e-03 2.096251e-02
5342 ENSG00000185909.15   9.348068  1 2.232207e-03 2.096593e-02
7778 ENSG00000130962.18  12.187730  2 2.256670e-03 2.116997e-02
5674 ENSG00000068305.18  16.623235  4 2.287365e-03 2.143192e-02
8388 ENSG00000205583.14  12.153227  2 2.295939e-03 2.144262e-02
4153 ENSG00000173226.17  12.151607  2 2.297799e-03 2.144262e-02
7571 ENSG00000204220.12  12.151553  2 2.297861e-03 2.144262e-02
9028  ENSG00000223756.8  16.611278  4 2.299603e-03 2.144262e-02
5717 ENSG00000109654.16  18.573008  5 2.307711e-03 2.149137e-02
3405 ENSG00000102290.23  12.140622  2 2.310454e-03 2.149137e-02
5279 ENSG00000183048.12  12.136539  2 2.315177e-03 2.149137e-02
6454 ENSG00000107560.12   9.280586  1 2.315953e-03 2.149137e-02
6577 ENSG00000099246.18  16.573958  4 2.338219e-03 2.167199e-02
2724  ENSG00000251201.8   9.226145  1 2.385835e-03 2.205244e-02
9704 ENSG00000196267.14  12.076260  2 2.386017e-03 2.205244e-02
2894 ENSG00000156931.16   9.224617  1 2.387826e-03 2.205244e-02
2682 ENSG00000151491.14  14.411181  3 2.395680e-03 2.209857e-02
777  ENSG00000116670.15   9.207401  1 2.410387e-03 2.220773e-02
8063  ENSG00000178935.5   9.200326  1 2.419721e-03 2.226507e-02
27   ENSG00000185495.10  12.044092  2 2.424704e-03 2.226507e-02
820  ENSG00000119321.10  14.383527  3 2.426974e-03 2.226507e-02
9640  ENSG00000267383.8   9.193218  1 2.429134e-03 2.226507e-02
998  ENSG00000126070.20  14.379985  3 2.431012e-03 2.226507e-02
373  ENSG00000100836.11   9.178477  1 2.448778e-03 2.240124e-02
4375 ENSG00000135317.14  12.015503  2 2.459612e-03 2.246044e-02
6298 ENSG00000177565.18  12.014327  2 2.461060e-03 2.246044e-02
7035 ENSG00000168275.16   9.146987  1 2.491279e-03 2.270942e-02
2417 ENSG00000144152.13  11.984191  2 2.498423e-03 2.274772e-02
4386 ENSG00000110497.15  11.957206  2 2.532361e-03 2.302959e-02
1265 ENSG00000132604.11   9.100685  1 2.555138e-03 2.320942e-02
4252 ENSG00000109956.13  14.250630  3 2.583111e-03 2.343597e-02
4689 ENSG00000132376.20  11.908110  2 2.595295e-03 2.351891e-02
7469 ENSG00000163873.10   9.065536  1 2.604722e-03 2.357670e-02
2019 ENSG00000071127.17   9.054087  1 2.621082e-03 2.369704e-02
6044 ENSG00000181450.18   9.046754  1 2.631617e-03 2.376448e-02
3030 ENSG00000160191.18   9.042878  1 2.637202e-03 2.378713e-02
8537 ENSG00000162923.17   9.035807  1 2.647422e-03 2.383029e-02
1877 ENSG00000092445.12  11.866920  2 2.649299e-03 2.383029e-02
1646 ENSG00000037280.16   9.033175  1 2.651235e-03 2.383029e-02
4136 ENSG00000172992.13  11.854659  2 2.665591e-03 2.393150e-02
954  ENSG00000124831.19  14.170725  3 2.681741e-03 2.403563e-02
6325 ENSG00000146828.18  14.167294  3 2.686059e-03 2.403563e-02
8483 ENSG00000232677.10  11.839019  2 2.686518e-03 2.403563e-02
8738 ENSG00000184319.17  16.258064  4 2.691727e-03 2.405439e-02
3856 ENSG00000168916.16  14.156730  3 2.699395e-03 2.406844e-02
8294  ENSG00000214756.8  14.156627  3 2.699526e-03 2.406844e-02
4026 ENSG00000116991.12  14.147647  3 2.710915e-03 2.414214e-02
6455 ENSG00000163946.14  11.805486  2 2.731940e-03 2.430138e-02
726  ENSG00000114857.19   8.967843  1 2.747728e-03 2.439960e-02
963  ENSG00000125375.18  11.792822  2 2.749295e-03 2.439960e-02
4307 ENSG00000168395.16   8.960526  1 2.758755e-03 2.445547e-02
6727 ENSG00000126804.14  11.782071  2 2.764113e-03 2.447491e-02
1678 ENSG00000176406.23  14.080305  3 2.797856e-03 2.474534e-02
3624 ENSG00000168056.18  16.144862  4 2.830815e-03 2.500823e-02
6183 ENSG00000109572.15  14.040921  3 2.849978e-03 2.514878e-02
4816 ENSG00000178209.17  11.713036  2 2.861189e-03 2.521892e-02
4779  ENSG00000177700.6   8.875163  1 2.890764e-03 2.545058e-02
2819 ENSG00000154783.12  11.667508  2 2.927069e-03 2.574089e-02
6894 ENSG00000122390.19  11.646833  2 2.957484e-03 2.596827e-02
8279  ENSG00000253846.3   8.832182  1 2.959644e-03 2.596827e-02
1718 ENSG00000119509.13  11.609131  2 3.013764e-03 2.641315e-02
5411 ENSG00000094631.21   8.789190  1 3.030208e-03 2.652719e-02
8778 ENSG00000196922.11  11.593202  2 3.037862e-03 2.656194e-02
570  ENSG00000107771.17  13.902406  3 3.041050e-03 2.656194e-02
351  ENSG00000100425.19   8.780074  1 3.045389e-03 2.656981e-02
6138 ENSG00000120899.18   8.774755  1 3.054283e-03 2.659262e-02
7872 ENSG00000168994.14   8.774396  1 3.054883e-03 2.659262e-02
6798 ENSG00000140511.12   8.768662  1 3.064501e-03 2.664634e-02
4476 ENSG00000125779.24  15.951659  4 3.084721e-03 2.679202e-02
3793  ENSG00000168672.4   8.715625  1 3.154943e-03 2.737117e-02
6824 ENSG00000196562.15   8.702738  1 3.177324e-03 2.753443e-02
6770 ENSG00000074582.15  13.798481  3 3.192692e-03 2.763663e-02
2935 ENSG00000157764.14   8.690207  1 3.199243e-03 2.763775e-02
2479 ENSG00000145390.12  13.793615  3 3.199972e-03 2.763775e-02
9747  ENSG00000276077.4  11.479882  2 3.214959e-03 2.766373e-02
133  ENSG00000010818.10   8.680831  1 3.215743e-03 2.766373e-02
1848 ENSG00000084234.18  11.479018  2 3.216348e-03 2.766373e-02
5741  ENSG00000261052.6  13.782081  3 3.217296e-03 2.766373e-02
5484 ENSG00000176473.14  11.474136  2 3.224208e-03 2.768946e-02
6620 ENSG00000196843.17   8.672433  1 3.230595e-03 2.768946e-02
7631 ENSG00000095739.11   8.670763  1 3.233557e-03 2.768946e-02
819  ENSG00000116977.19  11.467690  2 3.234617e-03 2.768946e-02
2925 ENSG00000157600.12  11.461930  2 3.243946e-03 2.773861e-02
3416 ENSG00000165689.17  11.450795  2 3.262057e-03 2.786265e-02
5705 ENSG00000153130.18  11.425319  2 3.303874e-03 2.818868e-02
2087 ENSG00000053108.17  13.706207  3 3.333596e-03 2.841092e-02
2123 ENSG00000104691.16   8.591840  1 3.376726e-03 2.874680e-02
6405 ENSG00000179454.14   8.585779  1 3.387984e-03 2.881091e-02
6814 ENSG00000197056.11  11.369113  2 3.398040e-03 2.886467e-02
9022 ENSG00000178971.16  11.338127  2 3.451096e-03 2.928317e-02
5067 ENSG00000185024.18  13.626170  3 3.460793e-03 2.932235e-02
7387 ENSG00000173269.14   8.545749  1 3.463300e-03 2.932235e-02
5712 ENSG00000188529.15  15.685997  4 3.470791e-03 2.935363e-02
121  ENSG00000005882.12  13.616289  3 3.476825e-03 2.937252e-02
2125 ENSG00000087460.29  11.311943  2 3.496574e-03 2.947758e-02
1595 ENSG00000072310.18  11.311764  2 3.496888e-03 2.947758e-02
867  ENSG00000121210.16  11.300270  2 3.517042e-03 2.961518e-02
6672 ENSG00000196730.13   8.513541  1 3.525134e-03 2.965102e-02
1924 ENSG00000058085.15   8.508282  1 3.535336e-03 2.970451e-02
7621 ENSG00000124313.18  13.571201  3 3.550923e-03 2.980308e-02
1142  ENSG00000243156.9  11.274394  2 3.562840e-03 2.987067e-02
5170 ENSG00000185261.15  11.241224  2 3.622423e-03 3.033730e-02
3880 ENSG00000169689.15  11.225331  2 3.651324e-03 3.054625e-02
8908 ENSG00000055163.20  13.475396  3 3.713600e-03 3.103016e-02
704  ENSG00000112983.18  11.188811  2 3.718610e-03 3.103016e-02
4074 ENSG00000113448.20   8.415082  1 3.721211e-03 3.103016e-02
4064 ENSG00000164162.14  13.466036  3 3.729884e-03 3.106499e-02
5183 ENSG00000184809.13  13.464006  3 3.733425e-03 3.106499e-02
6066 ENSG00000106290.16   8.399503  1 3.753237e-03 3.119626e-02
3420 ENSG00000122203.15   8.383951  1 3.785486e-03 3.143051e-02
6488 ENSG00000159199.14  13.423905  3 3.804060e-03 3.155084e-02
8480 ENSG00000231074.10  13.411403  3 3.826350e-03 3.170170e-02
4122 ENSG00000172534.14   8.360169  1 3.835348e-03 3.174223e-02
5795 ENSG00000187764.12   8.356253  1 3.843623e-03 3.177669e-02
2274 ENSG00000140836.17   8.329091  1 3.901517e-03 3.221551e-02
5    ENSG00000111186.13  11.090976  2 3.905036e-03 3.221551e-02
535  ENSG00000106069.24  11.078789  2 3.928906e-03 3.237787e-02
6198 ENSG00000141198.16  13.351862  3 3.934298e-03 3.238778e-02
3159 ENSG00000162714.13  11.063495  2 3.959065e-03 3.255699e-02
5916 ENSG00000184992.13  11.058268  2 3.969425e-03 3.260750e-02
6565 ENSG00000105576.16   8.278176  1 4.012442e-03 3.292588e-02
2924 ENSG00000046889.19   8.255118  1 4.063726e-03 3.325646e-02
5287 ENSG00000183621.15  13.281534  3 4.065689e-03 3.325646e-02
9006 ENSG00000007062.12  11.008248  2 4.069951e-03 3.325646e-02
2211 ENSG00000139372.15   8.250130  1 4.074907e-03 3.325646e-02
3696 ENSG00000186184.20   8.248190  1 4.079265e-03 3.325646e-02
2602 ENSG00000149269.10  11.002692  2 4.081275e-03 3.325646e-02
6136 ENSG00000104497.15  13.272519  3 4.082843e-03 3.325646e-02
3620 ENSG00000168004.10   8.227421  1 4.126211e-03 3.357433e-02
3792 ENSG00000172123.13   8.218042  1 4.147592e-03 3.371281e-02
4303 ENSG00000174238.16   8.197964  1 4.193741e-03 3.405212e-02
6271 ENSG00000122490.19   8.191660  1 4.208340e-03 3.413480e-02
3887 ENSG00000169727.13  10.932308  2 4.227459e-03 3.425394e-02
9221  ENSG00000247708.8  15.236949  4 4.234177e-03 3.427245e-02
2294 ENSG00000141179.14  10.917241  2 4.259428e-03 3.444077e-02
6344 ENSG00000143437.21  10.909576  2 4.275783e-03 3.453689e-02
6920 ENSG00000198901.14  10.880452  2 4.338503e-03 3.500692e-02
690  ENSG00000112559.15   8.116944  1 4.385342e-03 3.534796e-02
6785 ENSG00000174851.16   8.105811  1 4.412357e-03 3.552866e-02
3287 ENSG00000164039.15   8.091437  1 4.447488e-03 3.572260e-02
9133 ENSG00000177679.16   8.091221  1 4.448019e-03 3.572260e-02
7683 ENSG00000204599.15  13.087908  3 4.450305e-03 3.572260e-02
5074 ENSG00000171988.20   8.086540  1 4.459522e-03 3.572641e-02
3794 ENSG00000140987.21  13.082385  3 4.461788e-03 3.572641e-02
5938  ENSG00000188112.9   8.084459  1 4.464646e-03 3.572641e-02
1604 ENSG00000072415.10  13.077686  3 4.471582e-03 3.574491e-02
881  ENSG00000121964.15  13.070855  3 4.485855e-03 3.580381e-02
2464 ENSG00000145029.14  13.069729  3 4.488214e-03 3.580381e-02
2174 ENSG00000114378.17   8.069004  1 4.502885e-03 3.588382e-02
5294 ENSG00000182108.11   8.057843  1 4.530710e-03 3.606837e-02
9811  ENSG00000280623.1  10.784873  2 4.550872e-03 3.619161e-02
785  ENSG00000117385.16  10.762830  2 4.601307e-03 3.654928e-02
8371 ENSG00000108883.13  15.046714  4 4.605304e-03 3.654928e-02
1799 ENSG00000107951.15   8.023518  1 4.617380e-03 3.660754e-02
2941 ENSG00000185585.20   8.016592  1 4.635072e-03 3.671015e-02
6664 ENSG00000164022.18  15.026779  4 4.645998e-03 3.672967e-02
6215 ENSG00000132153.15   8.011922  1 4.647039e-03 3.672967e-02
2089 ENSG00000044090.13   8.006844  1 4.660088e-03 3.679518e-02
1375 ENSG00000115317.12  12.973594  3 4.694058e-03 3.699319e-02
2535 ENSG00000102225.17  12.971615  3 4.698395e-03 3.699319e-02
3709 ENSG00000172071.15  12.971099  3 4.699523e-03 3.699319e-02
6064  ENSG00000221923.9  10.692967  2 4.764876e-03 3.746947e-02
7850 ENSG00000172915.20   7.963442  1 4.773156e-03 3.749644e-02
6687 ENSG00000138119.17   7.961476  1 4.778342e-03 3.749907e-02
8042 ENSG00000146267.12  10.650372  2 4.867445e-03 3.815959e-02
4163 ENSG00000172687.14  10.648122  2 4.872925e-03 3.816384e-02
4004 ENSG00000160072.20  12.875977  3 4.912634e-03 3.843589e-02
7245 ENSG00000116396.15  10.586260  2 5.026004e-03 3.928313e-02
8431 ENSG00000213999.17  10.581106  2 5.038974e-03 3.934472e-02
1405 ENSG00000136014.12   7.854799  1 5.068599e-03 3.953610e-02
8654 ENSG00000104343.21  12.762798  3 5.178685e-03 4.035406e-02
539  ENSG00000106330.12   7.789968  1 5.253713e-03 4.089748e-02
9782  ENSG00000277067.4  10.494714  2 5.261406e-03 4.091616e-02
4538 ENSG00000163867.17   7.777957  1 5.288757e-03 4.108753e-02
9204  ENSG00000245958.7  20.111944  7 5.332895e-03 4.138884e-02
3659 ENSG00000172113.10  12.681159  3 5.379395e-03 4.170119e-02
3667 ENSG00000109919.10  10.448673  2 5.383931e-03 4.170119e-02
3685 ENSG00000075539.15  10.441260  2 5.403923e-03 4.181414e-02
5695 ENSG00000172500.13   7.735853  1 5.413499e-03 4.184635e-02
587  ENSG00000108587.16   7.724820  1 5.446679e-03 4.202589e-02
7328 ENSG00000162623.16  10.424545  2 5.449277e-03 4.202589e-02
6159 ENSG00000112242.16   7.722714  1 5.453036e-03 4.202589e-02
2847 ENSG00000155660.11   7.717976  1 5.467365e-03 4.209435e-02
1458 ENSG00000137177.20  12.640513  3 5.482173e-03 4.216637e-02
6126 ENSG00000127152.18   7.710828  1 5.489058e-03 4.217364e-02
6629 ENSG00000166822.13   7.709193  1 5.494030e-03 4.217364e-02
1534 ENSG00000120802.14   7.686001  1 5.565079e-03 4.267665e-02
6762 ENSG00000025039.15   7.665554  1 5.628498e-03 4.312021e-02
96    ENSG00000254951.7   7.658864  1 5.649406e-03 4.323753e-02
2426 ENSG00000118257.17  10.345339  2 5.669414e-03 4.333125e-02
6141 ENSG00000127870.17   7.651389  1 5.672863e-03 4.333125e-02
409  ENSG00000102265.12   7.645488  1 5.691451e-03 4.343032e-02
3082 ENSG00000161010.16  10.333999  2 5.701652e-03 4.346526e-02
7168 ENSG00000148773.14   7.621042  1 5.769116e-03 4.393622e-02
5089 ENSG00000185842.16   7.610454  1 5.803087e-03 4.415144e-02
8110 ENSG00000187109.15  14.499257  4 5.860852e-03 4.451746e-02
358  ENSG00000100504.17   7.592023  1 5.862713e-03 4.451746e-02
2531 ENSG00000146938.16  10.269116  2 5.889653e-03 4.467814e-02
9170 ENSG00000204152.14  10.252007  2 5.940252e-03 4.501371e-02
1555 ENSG00000158486.14   7.566736  1 5.945537e-03 4.501371e-02
2427 ENSG00000003400.15   7.550992  1 5.997703e-03 4.536423e-02
2160 ENSG00000096746.18   7.548100  1 6.007339e-03 4.537325e-02
5595 ENSG00000145335.17  12.442744  3 6.010634e-03 4.537325e-02
6631 ENSG00000178761.15  12.433638  3 6.036143e-03 4.552135e-02
7947 ENSG00000205763.14   7.531205  1 6.063935e-03 4.568637e-02
5895 ENSG00000104361.10   7.527542  1 6.076274e-03 4.573476e-02
7509 ENSG00000137409.20   7.513633  1 6.123375e-03 4.603776e-02
4732 ENSG00000114503.11   7.512143  1 6.128442e-03 4.603776e-02
3783 ENSG00000100731.16   7.508866  1 6.139602e-03 4.606632e-02
5047 ENSG00000176155.20  12.395495  3 6.144162e-03 4.606632e-02
5269 ENSG00000139117.14   7.451675  1 6.337745e-03 4.747168e-02
3568 ENSG00000109103.12  10.108181  2 6.383171e-03 4.774641e-02
4466 ENSG00000120885.22  10.107051  2 6.386777e-03 4.774641e-02
3311  ENSG00000164168.8   7.434016  1 6.400233e-03 4.780078e-02
6921 ENSG00000198728.11  10.092605  2 6.433075e-03 4.799968e-02
7202  ENSG00000118292.9   7.422544  1 6.441169e-03 4.801373e-02
6839 ENSG00000197102.14  12.274023  3 6.501065e-03 4.838185e-02
4095 ENSG00000119392.16   7.405336  1 6.503071e-03 4.838185e-02
3893 ENSG00000171574.18   7.398558  1 6.527617e-03 4.851777e-02
7738 ENSG00000125864.14   7.389827  1 6.559379e-03 4.870702e-02
8898  ENSG00000223891.7  16.097613  5 6.570840e-03 4.874529e-02
2660 ENSG00000150961.15   7.372551  1 6.622691e-03 4.908284e-02
5129 ENSG00000180881.20  14.217629  4 6.631907e-03 4.910406e-02
1836 ENSG00000113594.10   7.367077  1 6.642881e-03 4.910650e-02
5762 ENSG00000165792.18  12.226909  3 6.644942e-03 4.910650e-02
7400 ENSG00000107263.19   7.364192  1 6.653548e-03 4.912314e-02
5735 ENSG00000213023.11  10.018757  2 6.675051e-03 4.921805e-02
7806 ENSG00000101290.14   7.356185  1 6.683245e-03 4.921805e-02
155  ENSG00000059588.10   7.355577  1 6.685504e-03 4.921805e-02

length(idx)

[1] 1050

# Significant isoform results
idx.txp <- which(res.txp$adj_pvalue < 0.05)
res.txp[idx.txp,]

                 gene_id         feature_id         lr df       pvalue
20181 ENSG00000112759.19  ENST00000371755.9 288.822065  1 8.978826e-65
20182 ENSG00000112759.19  ENST00000393844.7 288.822065  1 8.978826e-65
13318 ENSG00000107554.17  ENST00000543621.6 179.903676  1 5.086884e-41
10876 ENSG00000172889.16  ENST00000371698.3 157.899284  1 3.255727e-36
10877 ENSG00000172889.16  ENST00000406555.7 157.899284  1 3.255727e-36
11418 ENSG00000164587.13  ENST00000312037.6 152.797864  1 4.240819e-35
15051 ENSG00000165629.20 ENST00000356708.12 127.371874  1 1.540307e-29
15050 ENSG00000165629.20  ENST00000335698.4 127.371874  1 1.540307e-29
14800 ENSG00000186635.15 ENST00000334211.12 126.273426  1 2.679072e-29
20211 ENSG00000159658.15  ENST00000674435.1 122.906969  1 1.461430e-28
10201 ENSG00000143344.16  ENST00000360851.4 118.855868  1 1.126227e-27
10200 ENSG00000143344.16  ENST00000304685.8 118.855868  1 1.126227e-27
3630  ENSG00000134853.12 ENST00000257290.10 113.834644  1 1.416411e-26
3631  ENSG00000134853.12  ENST00000507536.1 113.834644  1 1.416411e-26
15240 ENSG00000093167.18  ENST00000421276.6 112.120415  1 3.362546e-26
4948  ENSG00000026508.21  ENST00000433892.6 105.723697  1 8.476759e-25
13317 ENSG00000107554.17  ENST00000324109.9 100.531932  1 1.165035e-23
20718 ENSG00000001497.18  ENST00000374811.8  96.889531  1 7.330525e-23
7543  ENSG00000154380.18  ENST00000366843.7  95.611719  1 1.397765e-22
21528 ENSG00000196139.14  ENST00000380554.5  94.460322  1 2.500548e-22
15239 ENSG00000093167.18  ENST00000354379.8  91.533896  1 1.096969e-21
20078 ENSG00000024526.17  ENST00000456315.7  88.210201  1 5.885560e-21
20077 ENSG00000024526.17  ENST00000370966.9  88.210201  1 5.885560e-21
20748  ENSG00000204301.6  ENST00000491215.1  83.198896  1 7.419915e-20
181   ENSG00000153046.18  ENST00000397588.8  82.891759  1 8.667179e-20
15063 ENSG00000065613.15  ENST00000335753.8  82.109116  1 1.287773e-19
15064 ENSG00000065613.15  ENST00000369755.4  82.109116  1 1.287773e-19
16811 ENSG00000090989.18  ENST00000349598.6  77.652634  1 1.228524e-18
4483  ENSG00000129422.15  ENST00000693296.1  76.426957  1 2.285106e-18
5180  ENSG00000115318.12  ENST00000470907.6  75.163547  1 4.332935e-18
13015 ENSG00000119335.18  ENST00000686840.1  74.038529  1 7.660710e-18
19376 ENSG00000143469.20  ENST00000399639.6  73.997259  1 7.822559e-18
13013 ENSG00000119335.18 ENST00000322030.13  72.855704  1 1.394839e-17
2420  ENSG00000076248.11  ENST00000242576.7  70.375453  1 4.902620e-17
2421  ENSG00000076248.11  ENST00000336865.6  70.375453  1 4.902620e-17
15672 ENSG00000069869.17  ENST00000508075.1  67.122199  1 2.551887e-16
15671 ENSG00000069869.17  ENST00000435532.8  67.122199  1 2.551887e-16
16563 ENSG00000125354.24  ENST00000354228.8  65.776564  1 5.050525e-16
8818  ENSG00000163923.10  ENST00000296277.9  65.339936  1 6.303099e-16
8819  ENSG00000163923.10  ENST00000433055.1  65.339936  1 6.303099e-16
7209  ENSG00000038274.17 ENST00000321757.11  64.847789  1 8.091282e-16
7208  ENSG00000038274.17  ENST00000280969.9  64.847789  1 8.091282e-16
4946  ENSG00000026508.21 ENST00000263398.11  63.244676  1 1.825605e-15
7852  ENSG00000187672.14 ENST00000288221.11  58.031448  1 2.579608e-14
7853  ENSG00000187672.14  ENST00000486496.5  58.031448  1 2.579608e-14
14822 ENSG00000186439.14  ENST00000334268.9  57.561431  1 3.275865e-14
15398 ENSG00000107938.18  ENST00000337623.7  56.500519  1 5.618354e-14
5048  ENSG00000115109.14  ENST00000443124.5  56.044447  1 7.085104e-14
9648  ENSG00000167766.20  ENST00000536937.6  55.819684  1 7.943221e-14
6702  ENSG00000145555.15  ENST00000505695.5  55.731543  1 8.307460e-14
23244  ENSG00000225783.9  ENST00000620145.5  55.442961  1 9.621061e-14
18915 ENSG00000138326.21  ENST00000372360.9  54.629751  1 1.455160e-13
18916 ENSG00000138326.21  ENST00000613865.5  54.629751  1 1.455160e-13
19378 ENSG00000143469.20  ENST00000637265.1  53.090028  1 3.186059e-13
15879 ENSG00000125170.11  ENST00000340099.9  52.996673  1 3.341137e-13
8391  ENSG00000007392.17 ENST00000293872.13  51.535622  1 7.030973e-13
12615 ENSG00000134954.14  ENST00000535549.5  50.622131  1 1.119752e-12
18619 ENSG00000126883.18  ENST00000652454.1  50.547783  1 1.162985e-12
6481  ENSG00000143947.15  ENST00000404735.1  48.163361  1 3.921477e-12
6480  ENSG00000143947.15 ENST00000272317.11  48.163361  1 3.921477e-12
3534  ENSG00000134001.15  ENST00000466499.6  47.609077  1 5.202702e-12
20745  ENSG00000204301.6  ENST00000375023.3  47.559731  1 5.335326e-12
5178  ENSG00000115318.12  ENST00000393937.6  47.384876  1 5.833100e-12
1118  ENSG00000102471.15  ENST00000620924.1  46.882350  1 7.537852e-12
15006 ENSG00000187147.18  ENST00000355387.6  46.587146  1 8.763320e-12
15007 ENSG00000187147.18  ENST00000484745.5  46.587146  1 8.763320e-12
21530 ENSG00000196139.14  ENST00000605149.5  46.252863  1 1.039346e-11
7088  ENSG00000014216.16  ENST00000527323.5  45.961069  1 1.206264e-11
7087  ENSG00000014216.16 ENST00000279247.11  45.961069  1 1.206264e-11
12301 ENSG00000100280.17  ENST00000357586.7  45.928564  1 1.226446e-11
1744  ENSG00000111321.11  ENST00000228918.9  45.735987  1 1.353138e-11
1745  ENSG00000111321.11  ENST00000546296.5  45.735987  1 1.353138e-11
17087 ENSG00000168734.14  ENST00000372886.6  45.341265  1 1.655246e-11
722   ENSG00000088305.18  ENST00000328111.6  45.303951  1 1.687084e-11
723   ENSG00000088305.18  ENST00000348286.6  45.303951  1 1.687084e-11
16181 ENSG00000008130.15  ENST00000341426.9  45.014710  1 1.955599e-11
16182 ENSG00000008130.15  ENST00000341991.7  45.014710  1 1.955599e-11
16562 ENSG00000125354.24  ENST00000343984.5  44.730793  1 2.260738e-11
4354  ENSG00000103723.17  ENST00000642989.2  44.470752  1 2.581857e-11
10498  ENSG00000169750.9  ENST00000306897.9  44.465758  1 2.588451e-11
10499  ENSG00000169750.9  ENST00000580965.5  44.465758  1 2.588451e-11
18805 ENSG00000181885.18 ENST00000360325.11  44.359875  1 2.732303e-11
18806 ENSG00000181885.18  ENST00000397317.8  44.359875  1 2.732303e-11
10623 ENSG00000171992.13  ENST00000307662.5  44.260543  1 2.874521e-11
10624 ENSG00000171992.13  ENST00000519664.1  44.260543  1 2.874521e-11
14091 ENSG00000182287.15  ENST00000329235.6  43.683775  1 3.859583e-11
14824 ENSG00000186439.14  ENST00000546248.5  43.519098  1 4.198420e-11
16862 ENSG00000142192.21  ENST00000346798.8  43.375353  1 4.518437e-11
1112  ENSG00000102316.17  ENST00000375068.6  43.286514  1 4.728311e-11
1111  ENSG00000102316.17  ENST00000218439.8  43.286514  1 4.728311e-11
22233 ENSG00000109475.17  ENST00000394665.5  43.241723  1 4.837798e-11
1480  ENSG00000106484.16  ENST00000341441.9  42.957296  1 5.594786e-11
1479  ENSG00000106484.16 ENST00000223215.10  42.957296  1 5.594786e-11
401   ENSG00000031003.11  ENST00000689681.1  42.929937  1 5.673576e-11
17131 ENSG00000143612.21  ENST00000368518.5  42.262961  1 7.978947e-11
13275 ENSG00000137868.19  ENST00000395105.9  41.799678  1 1.011201e-10
23401  ENSG00000243004.7  ENST00000415499.5  41.450226  1 1.209106e-10
21618 ENSG00000101849.18  ENST00000407597.7  41.409390  1 1.234629e-10
8743  ENSG00000163697.17  ENST00000502841.5  41.240503  1 1.346043e-10
16810 ENSG00000090989.18 ENST00000346134.11  41.112373  1 1.437236e-10
16015 ENSG00000173262.12  ENST00000535295.5  41.109507  1 1.439345e-10
6782  ENSG00000146263.12  ENST00000511335.5  40.841761  1 1.650677e-10
10415 ENSG00000171634.19 ENST00000306378.11  40.576600  1 1.890572e-10
5623  ENSG00000122515.16 ENST00000265346.11  40.264643  1 2.217868e-10
18038 ENSG00000185963.14 ENST00000356884.11  40.185995  1 2.308976e-10
18039 ENSG00000185963.14  ENST00000375512.3  40.185995  1 2.308976e-10
7745  ENSG00000156482.11  ENST00000287038.8  40.085951  1 2.430306e-10
7746  ENSG00000156482.11  ENST00000521291.5  40.085951  1 2.430306e-10
12051 ENSG00000060237.19 ENST00000315939.11  39.733789  1 2.910463e-10
16702 ENSG00000036054.13  ENST00000344949.9  39.731681  1 2.913607e-10
16703 ENSG00000036054.13  ENST00000394144.9  39.731681  1 2.913607e-10
8723  ENSG00000163682.17 ENST00000295955.14  39.569967  1 3.165136e-10
2037  ENSG00000115486.13  ENST00000233838.9  39.518364  1 3.249888e-10
7544  ENSG00000154380.18  ENST00000366844.7  39.435728  1 3.390367e-10
180   ENSG00000153046.18          BambuTx53  39.342831  1 3.555560e-10
2899  ENSG00000128989.11  ENST00000566423.5  39.211646  1 3.802653e-10
2898  ENSG00000128989.11  ENST00000249822.9  39.211646  1 3.802653e-10
3293  ENSG00000131477.11 ENST00000253796.10  38.810453  1 4.670203e-10
22386 ENSG00000196417.13  ENST00000396408.8  38.789344  1 4.720981e-10
962   ENSG00000075413.19  ENST00000676938.1  38.490870  1 5.501043e-10
24977 ENSG00000240225.10  ENST00000490123.5  37.996196  1 7.088268e-10
15881 ENSG00000125170.11  ENST00000569548.5  37.951319  1 7.253200e-10
8394  ENSG00000007392.17  ENST00000490762.5  37.828311  1 7.725251e-10
18168 ENSG00000146540.15  ENST00000412051.5  37.762757  1 7.989256e-10
11592 ENSG00000180448.11  ENST00000313093.7  37.528512  1 9.008642e-10
6733  ENSG00000145817.17 ENST00000274496.10  37.352426  1 9.859817e-10
12170 ENSG00000168259.17  ENST00000457167.9  37.327684  1 9.985697e-10
12171 ENSG00000168259.17  ENST00000674214.1  37.327684  1 9.985697e-10
182   ENSG00000153046.18  ENST00000483019.1  37.190051  1 1.071591e-09
18398 ENSG00000205220.12  ENST00000358514.9  37.115589  1 1.113301e-09
22234 ENSG00000109475.17  ENST00000394667.8  37.093885  1 1.125762e-09
16858 ENSG00000102181.21  ENST00000346693.8  37.069016  1 1.140212e-09
16859 ENSG00000102181.21  ENST00000370377.8  37.069016  1 1.140212e-09
20209 ENSG00000159658.15  ENST00000371933.8  36.172560  1 1.805956e-09
20210 ENSG00000159658.15  ENST00000672422.2  36.172560  1 1.805956e-09
23243  ENSG00000225783.9  ENST00000616213.4  35.565384  1 2.466315e-09
17197 ENSG00000117448.14  ENST00000621846.4  35.168334  1 3.024010e-09
14329 ENSG00000151276.24  ENST00000621418.4  35.100401  1 3.131363e-09
14328 ENSG00000151276.24  ENST00000402939.7  35.100401  1 3.131363e-09
1718  ENSG00000110906.13 ENST00000228495.11  35.086375  1 3.154000e-09
1719  ENSG00000110906.13  ENST00000440541.6  35.086375  1 3.154000e-09
15716 ENSG00000164056.11  ENST00000651917.1  34.843307  1 3.573358e-09
19155 ENSG00000169851.15  ENST00000511884.6  34.606333  1 4.035911e-09
4252  ENSG00000102804.15  ENST00000261489.6  34.523627  1 4.211087e-09
4253  ENSG00000102804.15  ENST00000458659.3  34.523627  1 4.211087e-09
12052 ENSG00000060237.19  ENST00000535572.5  34.520106  1 4.218710e-09
17089 ENSG00000168734.14  ENST00000372894.7  34.243134  1 4.863886e-09
3923  ENSG00000136933.17  ENST00000394125.8  34.163768  1 5.066352e-09
22965  ENSG00000242028.8  ENST00000406925.6  34.060451  1 5.342619e-09
22966  ENSG00000242028.8  ENST00000442995.4  34.060451  1 5.342619e-09
15279 ENSG00000158555.15  ENST00000336898.8  33.905258  1 5.786210e-09
15280 ENSG00000158555.15  ENST00000529721.5  33.905258  1 5.786210e-09
17824 ENSG00000164209.17  ENST00000447245.6  33.684947  1 6.480019e-09
15276 ENSG00000100099.21  ENST00000439453.5  33.635339  1 6.647400e-09
15399 ENSG00000107938.18  ENST00000356792.9  33.569616  1 6.875845e-09
3533  ENSG00000134001.15 ENST00000256383.11  33.495321  1 7.143563e-09
13947  ENSG00000184014.9  ENST00000681203.1  33.456301  1 7.288329e-09
18873 ENSG00000111237.19 ENST00000360579.11  33.357973  1 7.666287e-09
22152 ENSG00000221955.11  ENST00000430155.6  33.324264  1 7.800330e-09
11479 ENSG00000137094.16  ENST00000454002.6  33.033262  1 9.059564e-09
11478 ENSG00000137094.16  ENST00000312316.9  33.033262  1 9.059564e-09
18617 ENSG00000126883.18 ENST00000359428.10  32.842708  1 9.992520e-09
15067 ENSG00000129353.15 ENST00000335757.10  32.722822  1 1.062820e-08
6854  ENSG00000133138.20  ENST00000481617.6  32.656920  1 1.099473e-08
6853  ENSG00000133138.20 ENST00000357242.10  32.656920  1 1.099473e-08
12577 ENSG00000166938.13  ENST00000319194.9  32.513380  1 1.183748e-08
16669 ENSG00000124614.16  ENST00000621356.3  32.490224  1 1.197936e-08
16670 ENSG00000124614.16  ENST00000648437.1  32.490224  1 1.197936e-08
19476 ENSG00000152818.19  ENST00000367526.8  32.370288  1 1.274199e-08
19477 ENSG00000152818.19  ENST00000367545.8  32.370288  1 1.274199e-08
8009  ENSG00000127603.32  ENST00000289893.8  32.285753  1 1.330856e-08
6734  ENSG00000145817.17  ENST00000448443.6  31.996010  1 1.544895e-08
166   ENSG00000164093.18          BambuTx40  31.933447  1 1.595462e-08
14124 ENSG00000184489.13  ENST00000520105.5  31.867342  1 1.650693e-08
14361 ENSG00000128951.14  ENST00000331200.8  31.851149  1 1.664512e-08
11295 ENSG00000137478.15 ENST00000311172.11  31.830555  1 1.682254e-08
11296 ENSG00000137478.15  ENST00000409418.9  31.830555  1 1.682254e-08
6799  ENSG00000112531.17  ENST00000361752.8  31.801651  1 1.707476e-08
16852 ENSG00000143369.15  ENST00000369047.9  31.780948  1 1.725774e-08
16853 ENSG00000143369.15  ENST00000470432.5  31.780948  1 1.725774e-08
4087  ENSG00000138162.19  ENST00000369001.5  31.689835  1 1.808663e-08
12613 ENSG00000134954.14  ENST00000392668.8  31.607033  1 1.887448e-08
16062 ENSG00000169398.19  ENST00000519993.5  31.573731  1 1.920094e-08
17613 ENSG00000135316.19 ENST00000355238.11  31.501420  1 1.992945e-08
13872 ENSG00000101974.15  ENST00000361648.6  31.456683  1 2.039395e-08
4947  ENSG00000026508.21  ENST00000425428.6  31.332068  1 2.174579e-08
17553 ENSG00000107518.18  ENST00000609571.5  31.239039  1 2.281320e-08
25614 ENSG00000196951.12  ENST00000608178.6  31.225680  1 2.297072e-08
9455  ENSG00000166847.10  ENST00000300087.7  31.162446  1 2.373129e-08
8365  ENSG00000161835.11  ENST00000293662.9  31.156548  1 2.380350e-08
5512  ENSG00000111846.20  ENST00000379597.7  31.137784  1 2.403471e-08
24735 ENSG00000165821.12  ENST00000614342.1  31.120813  1 2.424577e-08
24734 ENSG00000165821.12  ENST00000537235.2  31.120813  1 2.424577e-08
2290  ENSG00000070087.15 ENST00000239940.12  31.006805  1 2.571254e-08
2291  ENSG00000070087.15  ENST00000452853.6  31.006805  1 2.571254e-08
24078 ENSG00000119559.17  ENST00000586564.5  30.767026  1 2.909398e-08
23875  ENSG00000237515.9  ENST00000558583.3  30.615786  1 3.145242e-08
23874  ENSG00000237515.9  ENST00000423335.2  30.615786  1 3.145242e-08
18090 ENSG00000173209.23  ENST00000394457.7  30.542821  1 3.265781e-08
6574  ENSG00000144677.15  ENST00000443503.6  30.184504  1 3.928357e-08
6573  ENSG00000144677.15 ENST00000273179.10  30.184504  1 3.928357e-08
23806  ENSG00000228624.8  ENST00000517965.1  30.162645  1 3.972884e-08
11420 ENSG00000164587.13  ENST00000521466.5  29.814957  1 4.753108e-08
9272  ENSG00000166130.15  ENST00000299157.5  29.808301  1 4.769455e-08
23448  ENSG00000225953.4  ENST00000666719.2  29.774921  1 4.852286e-08
23449  ENSG00000225953.4  ENST00000668832.1  29.774921  1 4.852286e-08
22798 ENSG00000221978.13  ENST00000400809.8  29.682466  1 5.089308e-08
13725 ENSG00000179222.18 ENST00000326587.12  29.609283  1 5.285123e-08
13726 ENSG00000179222.18  ENST00000375772.7  29.609283  1 5.285123e-08
26433 ENSG00000167680.17  ENST00000586582.6  29.489774  1 5.621250e-08
8487  ENSG00000122417.15 ENST00000317336.11  29.425435  1 5.810995e-08
12544 ENSG00000143624.14  ENST00000481797.5  29.340667  1 6.070820e-08
18400 ENSG00000205220.12  ENST00000570985.1  29.298744  1 6.203588e-08
731   ENSG00000089009.16 ENST00000202773.14  29.276099  1 6.276513e-08
732   ENSG00000089009.16  ENST00000424576.6  29.276099  1 6.276513e-08
6452  ENSG00000143569.19  ENST00000428931.6  29.076844  1 6.956349e-08
3295  ENSG00000131477.11  ENST00000589683.5  28.798788  1 8.030133e-08
2313  ENSG00000108848.16  ENST00000240304.5  28.740621  1 8.274968e-08
20979 ENSG00000204576.12  ENST00000376557.3  28.690783  1 8.490687e-08
7349  ENSG00000152582.14 ENST00000282469.10  28.635998  1 8.734325e-08
7350  ENSG00000152582.14  ENST00000509059.5  28.635998  1 8.734325e-08
18260 ENSG00000182841.13  ENST00000357802.7  28.627788  1 8.771439e-08
13590 ENSG00000100614.18  ENST00000395076.9  28.527590  1 9.237280e-08
4508  ENSG00000055118.17  ENST00000532957.5  28.517113  1 9.287399e-08
2219   ENSG00000119640.9  ENST00000238618.8  28.220132  1 1.082725e-07
24150 ENSG00000133657.17  ENST00000645319.2  28.203129  1 1.092278e-07
7279  ENSG00000109670.16  ENST00000393956.9  28.082342  1 1.162618e-07
18274 ENSG00000138757.15  ENST00000359707.9  28.047101  1 1.183983e-07
24978 ENSG00000240225.10  ENST00000495307.5  27.960949  1 1.237885e-07
24969  ENSG00000241472.7  ENST00000664758.1  27.907739  1 1.272398e-07
10625 ENSG00000166377.21 ENST00000307671.12  27.740964  1 1.386945e-07
7619  ENSG00000155100.11  ENST00000617869.4  27.709900  1 1.409396e-07
12332 ENSG00000140538.16  ENST00000317501.7  27.684417  1 1.428085e-07
14362 ENSG00000128951.14  ENST00000455976.6  27.551354  1 1.529782e-07
17119 ENSG00000072518.22  ENST00000377810.8  27.435005  1 1.624637e-07
8724  ENSG00000163682.17  ENST00000449470.6  27.375194  1 1.675670e-07
15261 ENSG00000075420.13  ENST00000336824.8  27.332545  1 1.713038e-07
21581 ENSG00000205572.10  ENST00000514285.1  27.329787  1 1.715483e-07
8032  ENSG00000159079.19  ENST00000382549.8  27.135112  1 1.897206e-07
2344  ENSG00000114354.15  ENST00000240851.9  27.117341  1 1.914726e-07
22764  ENSG00000215375.6  ENST00000505477.5  27.076234  1 1.955878e-07
13281 ENSG00000156976.17 ENST00000323963.10  27.020991  1 2.012580e-07
4607  ENSG00000109046.15  ENST00000262394.7  27.020415  1 2.013179e-07
8602  ENSG00000163249.13  ENST00000392209.7  27.007262  1 2.026925e-07
3140  ENSG00000203485.14  ENST00000398337.8  26.992762  1 2.042187e-07
25369 ENSG00000245694.11  ENST00000557792.2  26.804625  1 2.250980e-07
18452 ENSG00000198561.16 ENST00000358694.10  26.579797  1 2.528743e-07
5047  ENSG00000115109.14 ENST00000263713.10  26.513593  1 2.616902e-07
6783  ENSG00000146263.12  ENST00000683635.1  26.372293  1 2.815504e-07
8222  ENSG00000160685.14  ENST00000368426.3  26.153456  1 3.153323e-07
22742 ENSG00000185201.18  ENST00000680197.1  26.148658  1 3.161167e-07
3848  ENSG00000136448.13  ENST00000592654.3  26.140295  1 3.174888e-07
8271  ENSG00000160917.15 ENST00000292476.10  26.098849  1 3.243773e-07
8272  ENSG00000160917.15  ENST00000436336.6  26.098849  1 3.243773e-07
17563 ENSG00000133961.21  ENST00000554546.5  26.096322  1 3.248021e-07
12399 ENSG00000134504.14  ENST00000580059.7  26.092895  1 3.253791e-07
16392 ENSG00000158321.18  ENST00000644939.1  25.937885  1 3.525812e-07
3544  ENSG00000134046.12  ENST00000256429.8  25.817022  1 3.753635e-07
9125  ENSG00000165156.15  ENST00000522655.5  25.780525  1 3.825289e-07
5697  ENSG00000003147.19  ENST00000406470.6  25.651694  1 4.089364e-07
22461  ENSG00000250151.9  ENST00000424442.5  25.630270  1 4.135017e-07
399   ENSG00000031003.11  ENST00000033079.7  25.612901  1 4.172404e-07
11593 ENSG00000180448.11  ENST00000543365.5  25.609076  1 4.180684e-07
16849 ENSG00000214063.12  ENST00000527644.2  25.569585  1 4.267128e-07
10692 ENSG00000217128.13  ENST00000510461.6  25.490127  1 4.446525e-07
10691 ENSG00000217128.13 ENST00000307968.11  25.490127  1 4.446525e-07
1987  ENSG00000003436.16  ENST00000421427.5  25.465286  1 4.504146e-07
10763 ENSG00000174099.12  ENST00000355192.8  25.463394  1 4.508566e-07
10762 ENSG00000174099.12 ENST00000308259.10  25.463394  1 4.508566e-07
19626 ENSG00000160710.18  ENST00000529168.2  25.453767  1 4.531119e-07
19625 ENSG00000160710.18  ENST00000368471.8  25.453767  1 4.531119e-07
11519 ENSG00000112763.17 ENST00000312541.10  25.342804  1 4.799395e-07
19950 ENSG00000067208.16  ENST00000370331.5  25.255725  1 5.021031e-07
9127  ENSG00000148187.18  ENST00000344641.8  25.217845  1 5.120621e-07
6175  ENSG00000141068.15  ENST00000644418.1  25.142257  1 5.325305e-07
11318 ENSG00000164114.19  ENST00000650955.1  25.138255  1 5.336368e-07
9124  ENSG00000165156.15  ENST00000395571.8  25.130381  1 5.358201e-07
20982 ENSG00000204576.12  ENST00000481741.5  25.002683  1 5.725058e-07
17823 ENSG00000164209.17  ENST00000355943.8  24.985370  1 5.776699e-07
16926 ENSG00000116698.22  ENST00000347615.6  24.801952  1 6.353311e-07
2794  ENSG00000127511.10 ENST00000248054.10  24.796045  1 6.372811e-07
2795  ENSG00000127511.10  ENST00000596802.5  24.796045  1 6.372811e-07
16352 ENSG00000107758.16  ENST00000394829.6  24.655745  1 6.854012e-07
8662  ENSG00000163513.19  ENST00000359013.4  24.615075  1 7.000197e-07
18655 ENSG00000168918.14  ENST00000445964.6  24.476911  1 7.520568e-07
24288 ENSG00000179715.13  ENST00000432328.2  24.278641  1 8.335831e-07
4319  ENSG00000038532.16  ENST00000261657.5  24.170635  1 8.816641e-07
14750 ENSG00000197928.11  ENST00000598513.6  24.058363  1 9.345945e-07
18453 ENSG00000198561.16  ENST00000529986.5  23.807764  1 1.064522e-06
21924 ENSG00000087152.16  ENST00000389384.8  23.763731  1 1.089156e-06
16063 ENSG00000169398.19  ENST00000521059.5  23.708360  1 1.120945e-06
16024 ENSG00000068366.21  ENST00000672401.1  23.641915  1 1.160324e-06
4720  ENSG00000100813.15  ENST00000605057.6  23.589492  1 1.192369e-06
17919 ENSG00000008838.21  ENST00000394126.5  23.574000  1 1.202008e-06
13871 ENSG00000101974.15  ENST00000327569.7  23.525349  1 1.232788e-06
10376  ENSG00000124134.9  ENST00000306117.5  23.486317  1 1.258053e-06
10377  ENSG00000124134.9  ENST00000537075.3  23.486317  1 1.258053e-06
10610 ENSG00000120549.18  ENST00000376454.8  23.478747  1 1.263013e-06
10611 ENSG00000120549.18  ENST00000458595.5  23.478747  1 1.263013e-06
9839  ENSG00000168522.13  ENST00000526755.5  23.478320  1 1.263293e-06
15129 ENSG00000101236.17 ENST00000358395.11  23.254276  1 1.419345e-06
15130 ENSG00000101236.17  ENST00000432261.6  23.254276  1 1.419345e-06
9837  ENSG00000168522.13  ENST00000302279.8  23.213476  1 1.449778e-06
22154 ENSG00000221955.11  ENST00000469902.6  23.210814  1 1.451787e-06
14166 ENSG00000184588.18  ENST00000371045.9  23.208381  1 1.453624e-06
14167 ENSG00000184588.18  ENST00000480109.2  23.208381  1 1.453624e-06
20567 ENSG00000119397.19  ENST00000373850.6  23.189941  1 1.467630e-06
3922  ENSG00000136933.17  ENST00000373538.8  23.165915  1 1.486081e-06
15328 ENSG00000169764.16 ENST00000337130.10  23.156333  1 1.493506e-06
15329 ENSG00000169764.16  ENST00000394417.7  23.156333  1 1.493506e-06
9649  ENSG00000167766.20  ENST00000541777.6  23.125457  1 1.517680e-06
5888  ENSG00000087470.19  ENST00000549701.6  23.102889  1 1.535598e-06
6881  ENSG00000147601.15 ENST00000276602.10  23.073849  1 1.558967e-06
5383  ENSG00000108306.13 ENST00000264658.11  23.010868  1 1.610881e-06
3437  ENSG00000132768.14  ENST00000495421.1  22.923058  1 1.686170e-06
2040  ENSG00000115486.13  ENST00000693287.1  22.727857  1 1.866425e-06
17038 ENSG00000146833.16  ENST00000349062.7  22.710574  1 1.883287e-06
17039 ENSG00000146833.16  ENST00000354241.5  22.710574  1 1.883287e-06
22387 ENSG00000196417.13  ENST00000504235.5  22.690095  1 1.903465e-06
8224  ENSG00000160685.14  ENST00000535420.6  22.551653  1 2.045685e-06
15102 ENSG00000130985.17 ENST00000335972.11  22.479683  1 2.123781e-06
15103 ENSG00000130985.17  ENST00000377351.8  22.479683  1 2.123781e-06
24697 ENSG00000183666.18  ENST00000607545.5  22.433548  1 2.175409e-06
12333 ENSG00000140538.16  ENST00000394480.6  22.423922  1 2.186338e-06
16911 ENSG00000130255.13  ENST00000347512.8  22.396126  1 2.218210e-06
744   ENSG00000090006.18 ENST00000308370.11  22.389715  1 2.225627e-06
13503 ENSG00000105443.16  ENST00000427476.4  22.316639  1 2.311946e-06
559   ENSG00000067840.13  ENST00000164640.8  22.310750  1 2.319048e-06
5457   ENSG00000105088.9  ENST00000593091.2  22.309158  1 2.320970e-06
15880 ENSG00000125170.11  ENST00000566936.5  22.304170  1 2.327007e-06
9456  ENSG00000166847.10  ENST00000563614.1  22.297382  1 2.335248e-06
10902  ENSG00000173905.9  ENST00000309027.4  22.226227  1 2.423408e-06
10903  ENSG00000173905.9  ENST00000470487.6  22.226227  1 2.423408e-06
1030  ENSG00000088833.18  ENST00000476071.5  22.218862  1 2.432722e-06
13292 ENSG00000108515.18  ENST00000519602.6  22.195870  1 2.462028e-06
14508 ENSG00000058673.17  ENST00000639812.1  22.121113  1 2.559788e-06
664   ENSG00000079156.17  ENST00000409631.5  21.931380  1 2.825753e-06
8764  ENSG00000163728.11  ENST00000412756.6  21.921915  1 2.839723e-06
25054  ENSG00000269743.3  ENST00000467290.1  21.921488  1 2.840356e-06
25055  ENSG00000269743.3  ENST00000594199.3  21.921488  1 2.840356e-06
4312  ENSG00000111450.14  ENST00000392373.7  21.905985  1 2.863395e-06
4311  ENSG00000111450.14 ENST00000261653.10  21.905985  1 2.863395e-06
24151 ENSG00000133657.17  ENST00000645538.1  21.729196  1 3.139762e-06
26288  ENSG00000262001.2  ENST00000573177.1  21.723851  1 3.148523e-06
2633  ENSG00000125637.16  ENST00000418251.6  21.696828  1 3.193189e-06
17734 ENSG00000079805.19  ENST00000408974.8  21.565951  1 3.418675e-06
16469 ENSG00000057663.16  ENST00000369070.5  21.565053  1 3.420276e-06
14095 ENSG00000182287.15  ENST00000673591.1  21.517740  1 3.505705e-06
16870 ENSG00000136754.18  ENST00000376166.5  21.509574  1 3.520666e-06
14367 ENSG00000182919.15  ENST00000528099.5  21.462913  1 3.607385e-06
16003 ENSG00000185630.19  ENST00000612123.3  21.423399  1 3.682495e-06
363   ENSG00000012061.16  ENST00000589165.5  21.422077  1 3.685037e-06
18110 ENSG00000122126.18  ENST00000371113.9  21.387398  1 3.752294e-06
18109 ENSG00000122126.18  ENST00000357121.5  21.387398  1 3.752294e-06
21990 ENSG00000140104.14  ENST00000389964.7  21.369521  1 3.787445e-06
4608  ENSG00000109046.15  ENST00000467843.6  21.329216  1 3.867914e-06
14063 ENSG00000184640.20  ENST00000427177.6  21.321458  1 3.883599e-06
11820 ENSG00000172785.18 ENST00000314367.14  21.286260  1 3.955565e-06
13319 ENSG00000107554.17  ENST00000636706.1  21.280629  1 3.967203e-06
478   ENSG00000061273.18  ENST00000354334.7  21.199014  1 4.139775e-06
11419 ENSG00000164587.13  ENST00000407193.7  21.157070  1 4.231374e-06
333   ENSG00000010270.14  ENST00000434197.5  21.084169  1 4.395446e-06
20572 ENSG00000118707.11  ENST00000373872.9  21.073542  1 4.419888e-06
20573 ENSG00000118707.11  ENST00000611732.4  21.073542  1 4.419888e-06
3325  ENSG00000089280.19  ENST00000487509.6  21.028721  1 4.524500e-06
17732 ENSG00000079805.19 ENST00000359692.10  21.000979  1 4.590486e-06
15068 ENSG00000129353.15  ENST00000407327.8  20.891804  1 4.859695e-06
7490  ENSG00000153904.21 ENST00000284031.13  20.886055  1 4.874301e-06
7491  ENSG00000153904.21  ENST00000426972.8  20.886055  1 4.874301e-06
9046  ENSG00000164830.19  ENST00000449762.6  20.853077  1 4.958950e-06
20236 ENSG00000160271.16  ENST00000372047.7  20.807301  1 5.078899e-06
1811  ENSG00000010810.17  ENST00000368667.6  20.789688  1 5.125823e-06
1994  ENSG00000114993.17 ENST00000272430.10  20.743720  1 5.250348e-06
17195 ENSG00000117448.14  ENST00000351829.9  20.738724  1 5.264062e-06
12781 ENSG00000177119.17 ENST00000320560.13  20.613032  1 5.621217e-06
12782 ENSG00000177119.17  ENST00000681817.1  20.613032  1 5.621217e-06
20560 ENSG00000180198.17  ENST00000373832.5  20.452307  1 6.113582e-06
5752  ENSG00000105865.11  ENST00000443233.5  20.433703  1 6.173301e-06
17926 ENSG00000087266.17  ENST00000435136.8  20.379667  1 6.350094e-06
14103 ENSG00000101361.17 ENST00000329276.10  20.352943  1 6.439398e-06
14104 ENSG00000101361.17  ENST00000492135.5  20.352943  1 6.439398e-06
3633  ENSG00000092421.17 ENST00000343348.11  20.311714  1 6.579654e-06
3632  ENSG00000092421.17 ENST00000257414.12  20.311714  1 6.579654e-06
21814 ENSG00000175161.14  ENST00000383699.8  20.248516  1 6.800620e-06
19686 ENSG00000197498.13  ENST00000425871.1  20.223806  1 6.889029e-06
19344 ENSG00000143353.12  ENST00000478794.5  20.133137  1 7.223428e-06
20938 ENSG00000204498.11  ENST00000376148.9  20.075400  1 7.444816e-06
113   ENSG00000101191.17  ENST00000266070.8  19.795134  1 8.620186e-06
10024 ENSG00000169057.24  ENST00000453960.7  19.758152  1 8.788602e-06
18138  ENSG00000244274.9  ENST00000360981.8  19.724113  1 8.946535e-06
10417 ENSG00000171634.19  ENST00000424123.7  19.685991  1 9.126800e-06
10731 ENSG00000175309.15 ENST00000308158.10  19.677044  1 9.169630e-06
21926 ENSG00000087152.16  ENST00000587097.6  19.637099  1 9.363335e-06
1986  ENSG00000003436.16  ENST00000392365.5  19.545368  1 9.823863e-06
1803  ENSG00000111790.14  ENST00000327214.5  19.492388  1 1.010013e-05
9011   ENSG00000164615.6  ENST00000678434.1  19.387280  1 1.067155e-05
22462  ENSG00000250151.9  ENST00000453882.1  19.263423  1 1.138670e-05
2761  ENSG00000126787.13  ENST00000247191.7  19.217652  1 1.166299e-05
2762  ENSG00000126787.13  ENST00000395425.6  19.217652  1 1.166299e-05
20568 ENSG00000119397.19  ENST00000373855.7  19.209178  1 1.171488e-05
9295  ENSG00000166169.17  ENST00000370162.8  19.176221  1 1.191889e-05
21043 ENSG00000136160.17  ENST00000626030.1  19.143154  1 1.212717e-05
12861 ENSG00000177302.15  ENST00000542570.5  19.117694  1 1.229002e-05
25416  ENSG00000250802.7  ENST00000642217.1  19.106207  1 1.236422e-05
20717 ENSG00000001497.18  ENST00000374807.9  19.081649  1 1.252434e-05
20719 ENSG00000001497.18  ENST00000677834.1  19.081648  1 1.252434e-05
21379 ENSG00000177189.14  ENST00000379565.9  19.059687  1 1.266930e-05
21380 ENSG00000177189.14  ENST00000646610.1  19.059687  1 1.266930e-05
19165 ENSG00000198839.10  ENST00000361822.8  19.053116  1 1.271300e-05
19166 ENSG00000198839.10  ENST00000361946.8  19.053116  1 1.271300e-05
15869 ENSG00000148498.16  ENST00000374794.8  19.033566  1 1.284391e-05
15247 ENSG00000172375.14  ENST00000648610.2  19.013601  1 1.297900e-05
3432  ENSG00000132749.11 ENST00000255087.10  18.975914  1 1.323791e-05
4859  ENSG00000120616.16 ENST00000319778.11  18.953935  1 1.339128e-05
4860  ENSG00000120616.16  ENST00000375110.6  18.953935  1 1.339128e-05
17025 ENSG00000176700.21  ENST00000690890.1  18.934099  1 1.353124e-05
6871  ENSG00000147526.20 ENST00000276520.12  18.901768  1 1.376251e-05
4481  ENSG00000129422.15  ENST00000381869.5  18.778631  1 1.468028e-05
40    ENSG00000140750.17 ENST00000289968.11  18.778166  1 1.468386e-05
9469  ENSG00000166881.10  ENST00000300128.9  18.751576  1 1.489003e-05
9470  ENSG00000166881.10  ENST00000379391.7  18.751576  1 1.489003e-05
19579 ENSG00000027869.12  ENST00000468744.5  18.751271  1 1.489240e-05
10316 ENSG00000121289.18  ENST00000591863.1  18.709572  1 1.522165e-05
9556  ENSG00000167323.12  ENST00000300737.8  18.707571  1 1.523763e-05
9557  ENSG00000167323.12  ENST00000526596.2  18.707571  1 1.523763e-05
1029  ENSG00000088833.18  ENST00000216879.9  18.697812  1 1.531581e-05
7192  ENSG00000151092.18  ENST00000417874.6  18.641495  1 1.577494e-05
11169 ENSG00000149187.19  ENST00000395290.6  18.595428  1 1.616077e-05
17465 ENSG00000197857.15  ENST00000355684.6  18.581782  1 1.627686e-05
17466 ENSG00000197857.15  ENST00000393337.7  18.581782  1 1.627686e-05
16159 ENSG00000172578.12  ENST00000487643.1  18.574204  1 1.634170e-05
17841  ENSG00000234719.9  ENST00000673243.1  18.545844  1 1.658665e-05
6727  ENSG00000145736.14  ENST00000517900.5  18.497102  1 1.701629e-05
21120 ENSG00000149474.15  ENST00000377681.8  18.401156  1 1.789494e-05
18562 ENSG00000196235.14  ENST00000432763.7  18.364023  1 1.824710e-05
22099 ENSG00000164889.15  ENST00000392826.6  18.356831  1 1.831611e-05
22100 ENSG00000164889.15  ENST00000413384.7  18.356831  1 1.831611e-05
21529 ENSG00000196139.14  ENST00000480822.5  18.291849  1 1.895164e-05
13274 ENSG00000137868.19  ENST00000323940.9  18.288352  1 1.898646e-05
23516 ENSG00000121671.12  ENST00000616080.2  18.224989  1 1.962865e-05
23517 ENSG00000121671.12  ENST00000616623.4  18.224989  1 1.962865e-05
8762  ENSG00000163728.11  ENST00000296015.9  18.160102  1 2.030892e-05
16360 ENSG00000111206.13  ENST00000359843.8  18.148842  1 2.042936e-05
9239   ENSG00000165916.9  ENST00000619920.4  18.106695  1 2.088657e-05
26464  ENSG00000197291.9  ENST00000589716.5  18.047155  1 2.155004e-05
25593  ENSG00000213777.5  ENST00000597004.1  18.028644  1 2.176061e-05
17623 ENSG00000100938.19  ENST00000355299.8  18.000487  1 2.208484e-05
5508  ENSG00000109586.12  ENST00000265000.9  17.913976  1 2.311177e-05
5509  ENSG00000109586.12  ENST00000505308.5  17.913976  1 2.311177e-05
7542  ENSG00000154380.18  ENST00000358675.6  17.766659  1 2.497213e-05
16022 ENSG00000068366.21  ENST00000502391.6  17.764262  1 2.500360e-05
4077  ENSG00000138078.16  ENST00000409957.5  17.741957  1 2.529848e-05
418   ENSG00000040608.14  ENST00000043402.8  17.706023  1 2.578091e-05
419   ENSG00000040608.14  ENST00000425986.1  17.706023  1 2.578091e-05
975   ENSG00000100528.12  ENST00000216416.9  17.661380  1 2.639314e-05
20542 ENSG00000204131.10  ENST00000631375.1  17.599700  1 2.726314e-05
20543 ENSG00000204131.10  ENST00000633930.2  17.599700  1 2.726314e-05
7881  ENSG00000148219.18  ENST00000341734.8  17.581274  1 2.752859e-05
3314  ENSG00000131759.18  ENST00000394081.7  17.549184  1 2.799709e-05
4718  ENSG00000100813.15  ENST00000457657.5  17.536734  1 2.818100e-05
9650  ENSG00000167766.20  ENST00000594682.6  17.503455  1 2.867860e-05
25230  ENSG00000245248.8  ENST00000660630.1  17.502467  1 2.869352e-05
25229  ENSG00000245248.8  ENST00000498979.7  17.502467  1 2.869352e-05
17208 ENSG00000128191.16  ENST00000351989.8  17.478035  1 2.906463e-05
9274  ENSG00000166130.15  ENST00000393042.3  17.477011  1 2.908029e-05
14499 ENSG00000156531.18  ENST00000625464.2  17.459209  1 2.935389e-05
17897 ENSG00000196498.13  ENST00000404121.6  17.451935  1 2.946642e-05
17898 ENSG00000196498.13  ENST00000405201.5  17.451935  1 2.946642e-05
18016 ENSG00000118518.17  ENST00000608991.5  17.436985  1 2.969907e-05
12971 ENSG00000109332.20 ENST00000349311.12  17.359672  1 3.093200e-05
20711 ENSG00000108094.17  ENST00000690393.1  17.352628  1 3.104686e-05
3256  ENSG00000131051.24  ENST00000463004.5  17.349869  1 3.109197e-05
4371  ENSG00000103876.14  ENST00000261755.9  17.283244  1 3.220139e-05
18262 ENSG00000182841.13  ENST00000458605.6  17.280761  1 3.224350e-05
2543  ENSG00000234465.11  ENST00000569031.6  17.249788  1 3.277342e-05
13040 ENSG00000111641.12  ENST00000399466.6  17.249727  1 3.277447e-05
13039 ENSG00000111641.12 ENST00000322166.10  17.249727  1 3.277447e-05
11836  ENSG00000181264.9  ENST00000531346.1  17.230784  1 3.310287e-05
21436 ENSG00000205726.15  ENST00000399349.5  17.206111  1 3.353559e-05
14543 ENSG00000169756.16  ENST00000393310.5  17.187581  1 3.386430e-05
14544 ENSG00000169756.16  ENST00000544547.5  17.187581  1 3.386430e-05
22814 ENSG00000132763.15  ENST00000401061.9  17.134714  1 3.482005e-05
22815 ENSG00000132763.15  ENST00000616135.1  17.134714  1 3.482005e-05
15604 ENSG00000168003.18 ENST00000338663.12  17.091243  1 3.562620e-05
17638 ENSG00000196776.17  ENST00000361309.6  17.087035  1 3.570522e-05
19819 ENSG00000148834.13 ENST00000369713.10  17.038246  1 3.663443e-05
19820 ENSG00000148834.13  ENST00000493946.1  17.038246  1 3.663443e-05
4642  ENSG00000064651.14  ENST00000262461.7  17.009166  1 3.719979e-05
4643  ENSG00000064651.14  ENST00000343225.4  17.009166  1 3.719979e-05
10474 ENSG00000172348.16 ENST00000306764.11  17.004753  1 3.728637e-05
10475 ENSG00000172348.16  ENST00000371374.6  17.004753  1 3.728637e-05
4527  ENSG00000104218.16 ENST00000262210.11  16.994435  1 3.748954e-05
5365  ENSG00000114251.15  ENST00000264634.9  16.974054  1 3.789415e-05
5366  ENSG00000114251.15  ENST00000474267.5  16.974054  1 3.789415e-05
19866 ENSG00000166272.18  ENST00000369889.5  16.959599  1 3.818377e-05
19867 ENSG00000166272.18  ENST00000448841.7  16.959599  1 3.818377e-05
20393 ENSG00000102384.14  ENST00000682095.1  16.948474  1 3.840819e-05
17988 ENSG00000160752.15  ENST00000467076.5  16.944606  1 3.848651e-05
3068  ENSG00000100364.19 ENST00000251993.11  16.906254  1 3.927198e-05
20639 ENSG00000096433.11  ENST00000374316.9  16.885689  1 3.969978e-05
20640 ENSG00000096433.11  ENST00000605930.3  16.885689  1 3.969978e-05
18561 ENSG00000196235.14 ENST00000359191.10  16.880455  1 3.980940e-05
18128 ENSG00000116560.11  ENST00000468598.5  16.863339  1 4.017002e-05
3259  ENSG00000131089.17 ENST00000253401.10  16.854446  1 4.035867e-05
16999 ENSG00000173267.14  ENST00000372017.4  16.838766  1 4.069349e-05
17000 ENSG00000173267.14  ENST00000483064.1  16.838766  1 4.069349e-05
20442 ENSG00000185513.17  ENST00000422861.3  16.832043  1 4.083789e-05
20443 ENSG00000185513.17  ENST00000648715.1  16.832043  1 4.083789e-05
15341 ENSG00000083312.19 ENST00000337273.10  16.785558  1 4.185061e-05
1757   ENSG00000111348.9  ENST00000228945.9  16.777677  1 4.202478e-05
1758   ENSG00000111348.9  ENST00000539131.1  16.777677  1 4.202478e-05
5630  ENSG00000075223.14  ENST00000265361.8  16.696749  1 4.385610e-05
5631  ENSG00000075223.14  ENST00000419255.6  16.696749  1 4.385610e-05
167   ENSG00000164093.18  ENST00000355080.9  16.680392  1 4.423587e-05
12992 ENSG00000137411.19  ENST00000676266.1  16.677127  1 4.431208e-05
11341 ENSG00000130349.10  ENST00000311381.8  16.650114  1 4.494762e-05
7916  ENSG00000137834.15  ENST00000612349.1  16.644186  1 4.508829e-05
7915  ENSG00000137834.15 ENST00000288840.10  16.644186  1 4.508829e-05
24079 ENSG00000119559.17  ENST00000588427.5  16.585843  1 4.649682e-05
16223 ENSG00000103168.17  ENST00000564208.5  16.582576  1 4.657699e-05
5661  ENSG00000004866.22  ENST00000393451.7  16.569917  1 4.688894e-05
6193  ENSG00000141314.13  ENST00000269051.9  16.534299  1 4.777796e-05
6194  ENSG00000141314.13  ENST00000536287.2  16.534299  1 4.777796e-05
2516  ENSG00000124140.15  ENST00000243964.7  16.532711  1 4.781799e-05
14801 ENSG00000186635.15  ENST00000393609.8  16.524886  1 4.801573e-05
21531 ENSG00000196139.14  ENST00000605781.5  16.505394  1 4.851186e-05
8361  ENSG00000161813.23  ENST00000398473.7  16.488576  1 4.894410e-05
13218 ENSG00000070814.22  ENST00000427724.7  16.477608  1 4.922807e-05
2460  ENSG00000123415.16  ENST00000508394.6  16.461295  1 4.965347e-05
4171  ENSG00000101670.12  ENST00000261292.9  16.298991  1 5.409276e-05
4211  ENSG00000109790.18  ENST00000504108.7  16.282377  1 5.456912e-05
4212  ENSG00000109790.18  ENST00000508137.6  16.282377  1 5.456912e-05
16566 ENSG00000125354.24  ENST00000394610.7  16.275867  1 5.475691e-05
12164 ENSG00000125779.24  ENST00000610179.7  16.253762  1 5.539949e-05
16179 ENSG00000125848.10  ENST00000341420.5  16.230981  1 5.606963e-05
16180 ENSG00000125848.10  ENST00000378053.3  16.230981  1 5.606963e-05
17894 ENSG00000008128.23  ENST00000460465.5  16.229415  1 5.611601e-05
9785  ENSG00000171016.13 ENST00000302000.10  16.201484  1 5.694949e-05
9073  ENSG00000164919.11  ENST00000520517.5  16.185649  1 5.742754e-05
9074  ENSG00000164919.11  ENST00000522934.5  16.185649  1 5.742754e-05
10820 ENSG00000172965.17  ENST00000658936.1  16.180477  1 5.758455e-05
19730 ENSG00000151923.18  ENST00000470781.5  16.149626  1 5.853013e-05
560   ENSG00000067840.13  ENST00000393758.7  16.133319  1 5.903621e-05
4245  ENSG00000092020.11 ENST00000261475.10  16.103608  1 5.996967e-05
20998 ENSG00000106772.19  ENST00000376717.6  16.095843  1 6.021606e-05
22958 ENSG00000185340.15  ENST00000621062.4  16.058362  1 6.141978e-05
14622  ENSG00000182057.5  ENST00000415205.2  16.053835  1 6.156681e-05
17098 ENSG00000132780.17  ENST00000350030.8  16.044535  1 6.186992e-05
5575  ENSG00000138802.11  ENST00000399100.6  16.042367  1 6.194082e-05
12626 ENSG00000141447.19  ENST00000319481.8  16.034973  1 6.218316e-05
19956 ENSG00000075826.17  ENST00000479697.5  15.964630  1 6.453706e-05
16351 ENSG00000107758.16  ENST00000394828.6  15.961719  1 6.463638e-05
17825 ENSG00000164209.17  ENST00000504098.1  15.942406  1 6.529922e-05
10311 ENSG00000112419.15  ENST00000367582.7  15.919676  1 6.608811e-05
10312 ENSG00000112419.15  ENST00000440869.7  15.919676  1 6.608811e-05
5511  ENSG00000111846.20  ENST00000316170.9  15.875095  1 6.766329e-05
10064 ENSG00000171735.19  ENST00000476163.5  15.800694  1 7.037669e-05
1672  ENSG00000109944.11 ENST00000307257.10  15.800576  1 7.038107e-05
16017 ENSG00000173262.12  ENST00000542546.5  15.790480  1 7.075764e-05
4529  ENSG00000104218.16  ENST00000678645.1  15.783231  1 7.102926e-05
18884 ENSG00000134884.15  ENST00000400198.8  15.770552  1 7.150686e-05
18885 ENSG00000134884.15  ENST00000472226.2  15.770552  1 7.150686e-05
8393  ENSG00000007392.17  ENST00000426094.5  15.743376  1 7.254150e-05
25613 ENSG00000196951.12  ENST00000512692.7  15.740064  1 7.266860e-05
15273 ENSG00000100099.21  ENST00000336873.9  15.734857  1 7.286894e-05
10785 ENSG00000164305.19  ENST00000523916.5  15.714527  1 7.365631e-05
10784 ENSG00000164305.19  ENST00000308394.9  15.714527  1 7.365631e-05
4352  ENSG00000103723.17  ENST00000535513.2  15.646449  1 7.635582e-05
23104  ENSG00000234741.9  ENST00000650796.1  15.638554  1 7.667524e-05
23006 ENSG00000071189.21  ENST00000428135.7  15.625084  1 7.722335e-05
5850  ENSG00000107864.15  ENST00000614585.4  15.612137  1 7.775392e-05
223    ENSG00000253507.6          BambuTx85  15.598690  1 7.830884e-05
23639 ENSG00000099810.21  ENST00000580900.5  15.572275  1 7.941050e-05
17360 ENSG00000170456.16 ENST00000389082.10  15.568963  1 7.954975e-05
17361 ENSG00000170456.16  ENST00000546299.1  15.568963  1 7.954975e-05
152   ENSG00000127483.19           BambuTx3  15.563742  1 7.976970e-05
13498 ENSG00000137473.19  ENST00000504425.5  15.558157  1 8.000572e-05
13497 ENSG00000137473.19  ENST00000325106.9  15.558157  1 8.000572e-05
15702 ENSG00000165246.15  ENST00000355905.6  15.545667  1 8.053601e-05
18953 ENSG00000197879.17  ENST00000648651.1  15.528543  1 8.126885e-05
3254  ENSG00000131051.24 ENST00000361162.10  15.525852  1 8.138461e-05
6450  ENSG00000143569.19 ENST00000271877.11  15.519971  1 8.163817e-05
16972 ENSG00000119139.21  ENST00000377245.9  15.494979  1 8.272470e-05
3457  ENSG00000141219.16  ENST00000359042.6  15.494435  1 8.274853e-05
187   ENSG00000124523.17 ENST00000379250.10  15.490270  1 8.293107e-05
13767 ENSG00000171606.18  ENST00000610905.4  15.440720  1 8.513397e-05
156    ENSG00000265992.1  ENST00000583516.1  15.438476  1 8.523509e-05
155    ENSG00000265992.1          BambuTx31  15.438476  1 8.523509e-05
1309  ENSG00000104852.15  ENST00000544278.2  15.431435  1 8.555326e-05
9296  ENSG00000166169.17  ENST00000370169.5  15.428595  1 8.568193e-05
11259 ENSG00000178821.13  ENST00000378602.3  15.420665  1 8.604223e-05
4747  ENSG00000035862.12  ENST00000585421.5  15.408456  1 8.659988e-05
4746  ENSG00000035862.12 ENST00000262768.11  15.408456  1 8.659988e-05
4054  ENSG00000137942.18 ENST00000260506.12  15.402739  1 8.686231e-05
4055  ENSG00000137942.18  ENST00000370253.6  15.402739  1 8.686231e-05
24631 ENSG00000151967.18  ENST00000482885.1  15.402441  1 8.687598e-05
6703  ENSG00000145555.15  ENST00000513610.6  15.401678  1 8.691107e-05
17968 ENSG00000105220.17  ENST00000588991.7  15.382983  1 8.777524e-05
4122  ENSG00000171681.13  ENST00000540793.5  15.350687  1 8.928847e-05
12043 ENSG00000114779.20 ENST00000361143.10  15.350060  1 8.931807e-05
18484 ENSG00000077458.13  ENST00000398187.6  15.301179  1 9.165928e-05
22617 ENSG00000104885.19  ENST00000398665.8  15.298171  1 9.180533e-05
22618 ENSG00000104885.19  ENST00000686010.1  15.298171  1 9.180533e-05
22886 ENSG00000049323.16  ENST00000407925.5  15.294656  1 9.197637e-05
17537 ENSG00000197586.13  ENST00000354989.9  15.271134  1 9.312887e-05
26301  ENSG00000284634.1  ENST00000642112.1  15.234698  1 9.494288e-05
11745 ENSG00000138668.19  ENST00000352301.8  15.229737  1 9.519261e-05
3589  ENSG00000134324.12  ENST00000256720.6  15.228031  1 9.527865e-05
3590  ENSG00000134324.12  ENST00000674199.1  15.228031  1 9.527865e-05
20394 ENSG00000102384.14  ENST00000684367.1  15.222889  1 9.553840e-05
18375 ENSG00000197448.14 ENST00000358406.10  15.219163  1 9.572709e-05
10491 ENSG00000172239.14  ENST00000306846.8  15.208433  1 9.627253e-05
10492 ENSG00000172239.14  ENST00000436644.6  15.208433  1 9.627253e-05
1602  ENSG00000108773.11 ENST00000225916.10  15.188967  1 9.727006e-05
1603  ENSG00000108773.11  ENST00000465682.5  15.188967  1 9.727006e-05
13276 ENSG00000137868.19  ENST00000432245.6  15.174450  1 9.802079e-05
24063 ENSG00000170381.14  ENST00000643230.2  15.129226  1 1.003969e-04
7080  ENSG00000125991.21  ENST00000496172.5  15.123862  1 1.006826e-04
7079  ENSG00000125991.21  ENST00000348547.7  15.123862  1 1.006826e-04
9683  ENSG00000167703.15 ENST00000301335.10  15.098556  1 1.020413e-04
5937  ENSG00000072041.18  ENST00000680379.1  15.086160  1 1.027136e-04
13282 ENSG00000156976.17  ENST00000425053.5  15.072155  1 1.034785e-04
19729 ENSG00000151923.18  ENST00000436547.7  15.071618  1 1.035080e-04
10732 ENSG00000175309.15  ENST00000476170.2  15.058019  1 1.042564e-04
16830 ENSG00000065534.20  ENST00000685953.1  15.042233  1 1.051320e-04
23168 ENSG00000212719.14  ENST00000653508.1  15.039154  1 1.053037e-04
39    ENSG00000140750.17         BambuTx130  15.004153  1 1.072748e-04
340   ENSG00000010219.14  ENST00000543431.6  14.984174  1 1.084166e-04
9238   ENSG00000165916.9  ENST00000602866.5  14.955770  1 1.100610e-04
17940 ENSG00000073921.18  ENST00000526033.5  14.941124  1 1.109187e-04
2314  ENSG00000108848.16  ENST00000393227.6  14.923727  1 1.119462e-04
10758 ENSG00000174136.13 ENST00000308234.11  14.916761  1 1.123603e-04
10759 ENSG00000174136.13  ENST00000513185.3  14.916761  1 1.123603e-04
4085  ENSG00000138162.19  ENST00000360561.7  14.900772  1 1.133166e-04
8894   ENSG00000164100.9  ENST00000296499.6  14.889556  1 1.139923e-04
8895   ENSG00000164100.9  ENST00000394488.2  14.889556  1 1.139923e-04
24016 ENSG00000237441.10  ENST00000437840.6  14.877601  1 1.147171e-04
7987  ENSG00000158604.15  ENST00000457408.7  14.867861  1 1.153109e-04
7988  ENSG00000158604.15  ENST00000481238.1  14.867861  1 1.153109e-04
7779  ENSG00000156925.12 ENST00000287538.10  14.836308  1 1.172562e-04
7780  ENSG00000156925.12  ENST00000370606.3  14.836308  1 1.172562e-04
18507 ENSG00000165280.18 ENST00000358901.11  14.827566  1 1.178009e-04
18508 ENSG00000165280.18  ENST00000679204.2  14.827566  1 1.178009e-04
15396 ENSG00000122565.19  ENST00000337620.8  14.822205  1 1.181363e-04
15397 ENSG00000122565.19  ENST00000396386.7  14.822205  1 1.181363e-04
24152  ENSG00000227398.5  ENST00000429315.3  14.813219  1 1.187006e-04
17099 ENSG00000132780.17  ENST00000351223.7  14.812291  1 1.187590e-04
23809  ENSG00000228624.8  ENST00000691803.1  14.777141  1 1.209934e-04
2227  ENSG00000119673.16 ENST00000238651.10  14.772459  1 1.212941e-04
24834 ENSG00000149260.18  ENST00000456580.6  14.759243  1 1.221473e-04
24835 ENSG00000149260.18  ENST00000648180.1  14.759243  1 1.221473e-04
14441 ENSG00000182541.18  ENST00000333611.8  14.758908  1 1.221689e-04
22356 ENSG00000185219.18  ENST00000396077.8  14.731705  1 1.239444e-04
22357 ENSG00000185219.18  ENST00000425708.6  14.731705  1 1.239444e-04
10663 ENSG00000100461.18  ENST00000399922.6  14.692208  1 1.265685e-04
4076  ENSG00000138078.16  ENST00000409936.5  14.656113  1 1.290156e-04
7626  ENSG00000155307.19  ENST00000647101.1  14.588936  1 1.336972e-04
23403  ENSG00000243004.7  ENST00000457921.6  14.581894  1 1.341978e-04
1812  ENSG00000010810.17  ENST00000368678.8  14.549050  1 1.365575e-04
10522 ENSG00000170234.13  ENST00000307063.9  14.530848  1 1.378832e-04
10523 ENSG00000170234.13  ENST00000456329.7  14.530848  1 1.378832e-04
5635  ENSG00000099250.18  ENST00000374822.8  14.510091  1 1.394108e-04
20562 ENSG00000180198.17  ENST00000683442.1  14.509623  1 1.394454e-04
11425 ENSG00000175216.15  ENST00000529230.6  14.488175  1 1.410422e-04
5538  ENSG00000113318.11  ENST00000265081.7  14.479260  1 1.417112e-04
5539  ENSG00000113318.11  ENST00000658259.1  14.479260  1 1.417112e-04
22393 ENSG00000100167.21  ENST00000644076.2  14.471552  1 1.422924e-04
15178 ENSG00000143702.16  ENST00000366542.6  14.466796  1 1.426521e-04
10808 ENSG00000048649.14 ENST00000308488.11  14.464381  1 1.428351e-04
20190 ENSG00000160345.13  ENST00000371789.7  14.427023  1 1.456966e-04
20191 ENSG00000160345.13  ENST00000429260.7  14.427023  1 1.456966e-04
4452  ENSG00000119707.14  ENST00000532683.5  14.415387  1 1.465996e-04
739    ENSG00000249115.9 ENST00000203166.10  14.394473  1 1.482368e-04
740    ENSG00000249115.9  ENST00000585968.5  14.394473  1 1.482368e-04
11251 ENSG00000115677.18  ENST00000391976.6  14.377098  1 1.496109e-04
11250 ENSG00000115677.18 ENST00000310931.10  14.377098  1 1.496109e-04
12925 ENSG00000177311.12  ENST00000321464.7  14.373924  1 1.498633e-04
12926 ENSG00000177311.12  ENST00000637056.1  14.373924  1 1.498633e-04
26904  ENSG00000283196.2  ENST00000636531.1  14.319801  1 1.542340e-04
13878 ENSG00000198040.11  ENST00000543758.5  14.315920  1 1.545523e-04
13877 ENSG00000198040.11  ENST00000539354.6  14.315920  1 1.545523e-04
10904 ENSG00000002330.14  ENST00000309032.8  14.274407  1 1.579986e-04
10905 ENSG00000002330.14  ENST00000394532.7  14.274407  1 1.579986e-04
15849 ENSG00000001631.17  ENST00000692807.1  14.272384  1 1.581685e-04
18635 ENSG00000169359.16  ENST00000643144.2  14.270509  1 1.583262e-04
9043  ENSG00000164830.19 ENST00000297447.10  14.265947  1 1.587103e-04
2345  ENSG00000114354.15  ENST00000490574.6  14.251697  1 1.599166e-04
13062 ENSG00000136709.12  ENST00000322313.9  14.220842  1 1.625601e-04
13063 ENSG00000136709.12  ENST00000409658.7  14.220842  1 1.625601e-04
10887 ENSG00000116991.12  ENST00000675407.1  14.192806  1 1.650002e-04
11315 ENSG00000164114.19  ENST00000311277.9  14.167602  1 1.672253e-04
13117 ENSG00000117335.20  ENST00000367042.6  14.165713  1 1.673932e-04
11705 ENSG00000166444.19  ENST00000532162.5  14.146469  1 1.691142e-04
18793 ENSG00000150636.17  ENST00000580292.2  14.139314  1 1.697587e-04
9763  ENSG00000085733.16 ENST00000301843.13  14.138665  1 1.698172e-04
9764  ENSG00000085733.16  ENST00000346329.7  14.138665  1 1.698172e-04
7610  ENSG00000154917.11  ENST00000285208.9  14.110615  1 1.723683e-04
7611  ENSG00000154917.11  ENST00000486858.5  14.110615  1 1.723683e-04
8750  ENSG00000163704.12  ENST00000412055.6  14.097740  1 1.735522e-04
8749  ENSG00000163704.12  ENST00000411976.2  14.097740  1 1.735522e-04
20633 ENSG00000158006.14  ENST00000374282.8  14.088552  1 1.744020e-04
20634 ENSG00000158006.14  ENST00000374284.5  14.088552  1 1.744020e-04
12582 ENSG00000107186.17  ENST00000536827.5  14.076288  1 1.755429e-04
12906 ENSG00000013441.17  ENST00000432425.5  14.073354  1 1.758170e-04
22864 ENSG00000108883.13  ENST00000591382.5  14.049818  1 1.780311e-04
20671 ENSG00000112514.18  ENST00000607266.5  14.030019  1 1.799153e-04
17499 ENSG00000004455.17  ENST00000373449.7  14.022249  1 1.806602e-04
12542 ENSG00000143624.14  ENST00000435409.6  14.013069  1 1.815444e-04
15494 ENSG00000068305.18  ENST00000557942.6  13.957954  1 1.869450e-04
24421 ENSG00000169855.21  ENST00000618846.4  13.943882  1 1.883496e-04
18958 ENSG00000158691.15  ENST00000684592.1  13.943579  1 1.883800e-04
10180 ENSG00000168958.20 ENST00000304593.14  13.884840  1 1.943599e-04
8603  ENSG00000163281.12  ENST00000295448.8  13.875218  1 1.953575e-04
2060  ENSG00000115806.13  ENST00000234160.5  13.867225  1 1.961902e-04
2061  ENSG00000115806.13  ENST00000442798.5  13.867225  1 1.961902e-04
22388 ENSG00000196417.13  ENST00000594030.2  13.866702  1 1.962448e-04
25975  ENSG00000257621.9  ENST00000554360.5  13.852010  1 1.977851e-04
21771 ENSG00000155269.12  ENST00000382487.5  13.851950  1 1.977914e-04
21772 ENSG00000155269.12  ENST00000513120.2  13.851950  1 1.977914e-04
5384  ENSG00000108306.13  ENST00000394294.7  13.843261  1 1.987081e-04
10398 ENSG00000168916.16  ENST00000504926.5  13.821237  1 2.010509e-04
17920 ENSG00000008838.21  ENST00000394128.7  13.814373  1 2.017867e-04
27032  ENSG00000288663.1  ENST00000679196.1  13.798452  1 2.035039e-04
14880 ENSG00000109184.15  ENST00000477560.5  13.781079  1 2.053944e-04
5493   ENSG00000114107.9  ENST00000481834.5  13.766597  1 2.069839e-04
22385 ENSG00000187735.15  ENST00000640382.1  13.750788  1 2.087332e-04
18189 ENSG00000112200.17  ENST00000370708.8  13.726572  1 2.114417e-04
18791 ENSG00000150636.17  ENST00000360242.9  13.701260  1 2.143106e-04
16110 ENSG00000055732.13  ENST00000370589.7  13.681897  1 2.165318e-04
12062 ENSG00000107957.17  ENST00000692756.1  13.637038  1 2.217670e-04
3514  ENSG00000133812.18 ENST00000256190.13  13.627921  1 2.228465e-04
3515  ENSG00000133812.18  ENST00000689128.1  13.627921  1 2.228465e-04
16660 ENSG00000127616.20  ENST00000647230.1  13.591019  1 2.272702e-04
13782 ENSG00000157216.16  ENST00000371319.8  13.568103  1 2.300617e-04
16543 ENSG00000129691.16  ENST00000428278.6  13.567275  1 2.301632e-04
16542 ENSG00000129691.16 ENST00000343823.11  13.567275  1 2.301632e-04
6678   ENSG00000145375.9  ENST00000422835.2  13.560654  1 2.309766e-04
4717  ENSG00000100813.15  ENST00000357481.6  13.556398  1 2.315009e-04
6174  ENSG00000141068.15  ENST00000398988.7  13.551918  1 2.320542e-04
24726  ENSG00000223756.8  ENST00000533775.6  13.550712  1 2.322033e-04
23919 ENSG00000184319.17  ENST00000686213.1  13.533141  1 2.343874e-04
5198  ENSG00000082258.13  ENST00000419781.5  13.516833  1 2.364331e-04
9044  ENSG00000164830.19 ENST00000312046.10  13.515300  1 2.366263e-04
1507  ENSG00000106692.15  ENST00000223528.6  13.509885  1 2.373101e-04
2784  ENSG00000130803.15 ENST00000247956.11  13.488843  1 2.399862e-04
2785  ENSG00000130803.15  ENST00000360385.7  13.488843  1 2.399862e-04
17591 ENSG00000133104.14  ENST00000438666.7  13.466071  1 2.429165e-04
10662 ENSG00000100461.18  ENST00000359890.8  13.462869  1 2.433314e-04
9539  ENSG00000167191.12  ENST00000569479.5  13.445935  1 2.455376e-04
19265 ENSG00000160691.19  ENST00000368445.9  13.440123  1 2.462995e-04
2924  ENSG00000129255.16 ENST00000250124.11  13.430351  1 2.475858e-04
2925  ENSG00000129255.16  ENST00000574558.1  13.430351  1 2.475858e-04
18068 ENSG00000099246.18  ENST00000682852.1  13.424767  1 2.483238e-04
17840  ENSG00000234719.9  ENST00000540412.1  13.411046  1 2.501468e-04
17987 ENSG00000160752.15  ENST00000447866.5  13.407165  1 2.506650e-04
8607  ENSG00000152795.18  ENST00000602300.5  13.403984  1 2.510904e-04
8606  ENSG00000152795.18  ENST00000507721.5  13.403984  1 2.510904e-04
22941 ENSG00000164199.18  ENST00000425867.3  13.400078  1 2.516138e-04
10300 ENSG00000187741.15  ENST00000568369.5  13.395417  1 2.522398e-04
5886  ENSG00000087470.19  ENST00000452533.6  13.352143  1 2.581275e-04
2824  ENSG00000127824.15  ENST00000248437.9  13.325499  1 2.618212e-04
2825  ENSG00000127824.15  ENST00000498660.1  13.325499  1 2.618212e-04
7740  ENSG00000156453.14  ENST00000357517.6  13.311786  1 2.637430e-04
147   ENSG00000131375.10          BambuTx28  13.290845  1 2.667052e-04
148   ENSG00000131375.10  ENST00000253693.7  13.290845  1 2.667052e-04
17075 ENSG00000166833.23  ENST00000396085.6  13.290039  1 2.668199e-04
14580 ENSG00000182718.18  ENST00000451270.7  13.285965  1 2.674004e-04
14579 ENSG00000182718.18  ENST00000421017.6  13.285965  1 2.674004e-04
2517  ENSG00000124140.15  ENST00000413737.2  13.283153  1 2.678017e-04
7973  ENSG00000005187.12  ENST00000614721.1  13.268327  1 2.699279e-04
3573  ENSG00000134285.11  ENST00000550765.6  13.248054  1 2.728631e-04
13438 ENSG00000116191.19  ENST00000367634.7  13.245435  1 2.732445e-04
13439 ENSG00000116191.19  ENST00000367635.8  13.245435  1 2.732445e-04
17014 ENSG00000100241.22  ENST00000684986.1  13.205534  1 2.791236e-04
16925 ENSG00000109572.15  ENST00000613795.4  13.185420  1 2.821355e-04
10469 ENSG00000144354.14  ENST00000306721.8  13.153831  1 2.869320e-04
10753 ENSG00000174628.16  ENST00000568300.6  13.148699  1 2.877190e-04
22005  ENSG00000212123.4  ENST00000390672.2  13.132981  1 2.901428e-04
22006  ENSG00000212123.4  ENST00000419421.3  13.132981  1 2.901428e-04
17328 ENSG00000146828.18  ENST00000354161.8  13.117096  1 2.926133e-04
21264 ENSG00000138050.15  ENST00000505747.6  13.109993  1 2.937248e-04
22140 ENSG00000187109.15  ENST00000548044.5  13.109677  1 2.937743e-04
15177 ENSG00000143702.16  ENST00000336415.8  13.109519  1 2.937991e-04
16726 ENSG00000181852.18  ENST00000615206.4  13.096915  1 2.957824e-04
23402  ENSG00000243004.7  ENST00000449573.5  13.080772  1 2.983425e-04
21230 ENSG00000182220.15  ENST00000638153.1  13.060869  1 3.015295e-04
13279 ENSG00000168952.16  ENST00000396700.5  13.047209  1 3.037367e-04
25578  ENSG00000281501.1  ENST00000507794.2  13.032966  1 3.060554e-04
25579  ENSG00000281501.1  ENST00000510415.1  13.032966  1 3.060554e-04
15180 ENSG00000157823.17  ENST00000336418.9  12.964170  1 3.175092e-04
951   ENSG00000239900.14  ENST00000636714.1  12.960215  1 3.181806e-04
17179 ENSG00000169062.15  ENST00000475218.2  12.941853  1 3.213168e-04
24064 ENSG00000170381.14  ENST00000643441.1  12.930365  1 3.232948e-04
9858  ENSG00000172113.10  ENST00000442597.6  12.914724  1 3.260075e-04
23096 ENSG00000136279.21  ENST00000448521.6  12.874628  1 3.330670e-04
18212 ENSG00000178761.15 ENST00000357635.10  12.868393  1 3.341784e-04
17120 ENSG00000072518.22  ENST00000402010.8  12.857224  1 3.361790e-04
1798  ENSG00000111725.11  ENST00000541640.5  12.842133  1 3.389011e-04
16912 ENSG00000130255.13  ENST00000394580.2  12.832212  1 3.407027e-04
9517  ENSG00000167085.13  ENST00000512041.7  12.826355  1 3.417710e-04
9516  ENSG00000167085.13  ENST00000300408.8  12.826355  1 3.417710e-04
10114 ENSG00000157985.19  ENST00000614409.4  12.794781  1 3.475877e-04
18167 ENSG00000146540.15 ENST00000357429.10  12.792449  1 3.480212e-04
17776 ENSG00000182534.14  ENST00000449428.7  12.792099  1 3.480863e-04
14529 ENSG00000173482.17  ENST00000580170.6  12.782395  1 3.498967e-04
3116   ENSG00000130035.9  ENST00000541339.2  12.765688  1 3.530356e-04
7001  ENSG00000213593.10  ENST00000278422.9  12.754858  1 3.550858e-04
7002  ENSG00000213593.10  ENST00000378312.8  12.754858  1 3.550858e-04
22650  ENSG00000214756.8  ENST00000532971.2  12.744949  1 3.569719e-04
21736 ENSG00000104723.21  ENST00000503731.6  12.739702  1 3.579747e-04
22135 ENSG00000133640.20  ENST00000393217.7  12.721462  1 3.614832e-04
23097 ENSG00000136279.21  ENST00000494774.5  12.660748  1 3.734128e-04
10447 ENSG00000141524.17  ENST00000392467.7  12.624773  1 3.806681e-04
24911  ENSG00000219626.9  ENST00000469867.1  12.617610  1 3.821297e-04
18513 ENSG00000008311.16  ENST00000417368.7  12.611091  1 3.834646e-04
18514 ENSG00000008311.16  ENST00000681708.1  12.611091  1 3.834646e-04
17739 ENSG00000187239.17  ENST00000420781.5  12.609099  1 3.838734e-04
3718  ENSG00000135636.15  ENST00000410020.8  12.565361  1 3.929628e-04
6872  ENSG00000147526.20  ENST00000317827.9  12.560314  1 3.940255e-04
10626 ENSG00000166377.21  ENST00000426216.6  12.553125  1 3.955444e-04
5034  ENSG00000094975.14  ENST00000263688.4  12.526433  1 4.012351e-04
16666 ENSG00000147316.15  ENST00000689633.1  12.519437  1 4.027402e-04
25510 ENSG00000001084.13  ENST00000616923.5  12.510617  1 4.046459e-04
15731 ENSG00000165792.18  ENST00000382985.8  12.505947  1 4.056587e-04
18140  ENSG00000244274.9  ENST00000372723.7  12.482885  1 4.106973e-04
18218 ENSG00000197563.11  ENST00000638183.1  12.447079  1 4.186461e-04
1499  ENSG00000081386.13  ENST00000375231.5  12.446401  1 4.187980e-04
1498  ENSG00000081386.13  ENST00000223428.9  12.446401  1 4.187980e-04
24221 ENSG00000100888.15  ENST00000557364.6  12.424160  1 4.238150e-04
15409 ENSG00000076928.18  ENST00000337665.8  12.421080  1 4.245146e-04
17819 ENSG00000159199.14  ENST00000355938.9  12.385518  1 4.326766e-04
11077 ENSG00000154889.17  ENST00000589731.5  12.361475  1 4.382843e-04
18775 ENSG00000197102.14  ENST00000681283.1  12.332396  1 4.451647e-04
18924 ENSG00000122390.19  ENST00000575076.5  12.323428  1 4.473085e-04
11407 ENSG00000092108.22  ENST00000458591.7  12.320628  1 4.479799e-04
11408 ENSG00000092108.22  ENST00000544052.6  12.320628  1 4.479799e-04
18006 ENSG00000196531.14  ENST00000393891.8  12.300261  1 4.528949e-04
21150 ENSG00000122707.12  ENST00000377966.4  12.292162  1 4.548646e-04
21151 ENSG00000122707.12  ENST00000479053.1  12.292162  1 4.548646e-04
24509 ENSG00000137601.18  ENST00000510533.5  12.271872  1 4.598369e-04
24308  ENSG00000235437.9  ENST00000609401.6  12.250863  1 4.650431e-04
9416  ENSG00000166716.10  ENST00000560079.7  12.249793  1 4.653097e-04
9415  ENSG00000166716.10  ENST00000559607.1  12.249793  1 4.653097e-04
3530  ENSG00000133997.12 ENST00000256379.10  12.248246  1 4.656956e-04
3434  ENSG00000132749.11  ENST00000443940.6  12.247391  1 4.659091e-04
9172  ENSG00000102290.23 ENST00000298274.12  12.238987  1 4.680124e-04
15691  ENSG00000189136.9  ENST00000558251.5  12.234765  1 4.690726e-04
1061  ENSG00000172264.18  ENST00000483997.5  12.190216  1 4.804082e-04
1062  ENSG00000172264.18  ENST00000684519.1  12.190216  1 4.804082e-04
17468 ENSG00000122566.22  ENST00000618183.5  12.178008  1 4.835627e-04
7957  ENSG00000102024.19  ENST00000355899.8  12.176791  1 4.838782e-04
7958  ENSG00000102024.19  ENST00000539310.5  12.176791  1 4.838782e-04
635   ENSG00000064763.12  ENST00000686305.1  12.164115  1 4.871778e-04
5737  ENSG00000071242.12  ENST00000265678.9  12.163394  1 4.873660e-04
5738  ENSG00000071242.12  ENST00000510118.5  12.163394  1 4.873660e-04
10799 ENSG00000138138.14 ENST00000308448.11  12.142959  1 4.927352e-04
8183  ENSG00000160310.19 ENST00000291705.11  12.139257  1 4.937143e-04
4154  ENSG00000118600.13 ENST00000261234.11  12.067945  1 5.129621e-04
26576 ENSG00000196267.14  ENST00000597252.5  12.051356  1 5.175472e-04
21603 ENSG00000145740.20  ENST00000396591.8  12.046836  1 5.188036e-04
21602 ENSG00000145740.20  ENST00000380860.8  12.046836  1 5.188036e-04
1993  ENSG00000114993.17  ENST00000233330.6  12.046707  1 5.188396e-04
1063  ENSG00000101276.18 ENST00000217254.11  12.037713  1 5.213491e-04
24699 ENSG00000183666.18  ENST00000685932.1  12.002306  1 5.313477e-04
16366 ENSG00000124104.19  ENST00000491381.6  11.988642  1 5.352577e-04
9132  ENSG00000165219.23 ENST00000312123.13  11.953534  1 5.454382e-04
10570 ENSG00000170266.16  ENST00000399402.7  11.945958  1 5.476607e-04
10569 ENSG00000170266.16 ENST00000307363.10  11.945958  1 5.476607e-04
17554 ENSG00000107518.18  ENST00000650603.1  11.941678  1 5.489202e-04
17831 ENSG00000204681.11  ENST00000377012.8  11.935708  1 5.506820e-04
16985 ENSG00000157450.16  ENST00000557998.5  11.927758  1 5.530370e-04
15410 ENSG00000076928.18  ENST00000354532.8  11.922264  1 5.546703e-04
18583 ENSG00000074582.15  ENST00000359273.8  11.916881  1 5.562755e-04
4462  ENSG00000110911.17  ENST00000262052.9  11.906300  1 5.594441e-04
4463  ENSG00000110911.17  ENST00000644495.1  11.906300  1 5.594441e-04
14649 ENSG00000186814.14 ENST00000333206.10  11.904525  1 5.599774e-04
26328  ENSG00000266412.6  ENST00000581486.6  11.900996  1 5.610395e-04
26329  ENSG00000266412.6  ENST00000585132.5  11.900996  1 5.610395e-04
8574  ENSG00000163075.13  ENST00000598644.5  11.897929  1 5.619641e-04
19154 ENSG00000169851.15  ENST00000361762.3  11.896955  1 5.622578e-04
5572  ENSG00000138798.13  ENST00000509793.5  11.890167  1 5.643107e-04
5064  ENSG00000092445.12  ENST00000263798.8  11.886764  1 5.653427e-04
14587 ENSG00000185187.13  ENST00000527987.1  11.865023  1 5.719806e-04
632   ENSG00000065883.17  ENST00000646039.1  11.863337  1 5.724988e-04
12874 ENSG00000010244.19  ENST00000394673.6  11.858453  1 5.740020e-04
2372  ENSG00000121964.15  ENST00000344850.8  11.857541  1 5.742831e-04
9228  ENSG00000165795.25  ENST00000397853.7  11.852848  1 5.757322e-04
17834 ENSG00000196233.14  ENST00000371103.8  11.841486  1 5.792558e-04
17835 ENSG00000196233.14  ENST00000421806.4  11.841486  1 5.792558e-04
26878  ENSG00000279765.3  ENST00000629685.2  11.838530  1 5.801762e-04
26879  ENSG00000279765.3  ENST00000630790.1  11.838530  1 5.801762e-04
5598  ENSG00000113645.15  ENST00000524038.5  11.807454  1 5.899405e-04
2577  ENSG00000124831.19 ENST00000308482.14  11.795651  1 5.936926e-04
24707  ENSG00000237638.3  ENST00000666526.2  11.758608  1 6.056250e-04
24708  ENSG00000237638.3  ENST00000685506.1  11.758608  1 6.056250e-04
4641  ENSG00000119509.13  ENST00000374921.3  11.733283  1 6.139221e-04
14419 ENSG00000183048.12  ENST00000573246.1  11.723173  1 6.172663e-04
3681  ENSG00000135424.19 ENST00000257879.11  11.723040  1 6.173103e-04
4485  ENSG00000085415.16  ENST00000399892.7  11.669900  1 6.351944e-04
4484  ENSG00000085415.16 ENST00000262124.15  11.669900  1 6.351944e-04
735   ENSG00000089063.15 ENST00000202834.11  11.668884  1 6.355411e-04
736   ENSG00000089063.15  ENST00000379299.6  11.668884  1 6.355411e-04
13110 ENSG00000178209.17  ENST00000345136.8  11.668439  1 6.356933e-04
19326 ENSG00000143756.12 ENST00000366862.10  11.649517  1 6.421920e-04
19327 ENSG00000143756.12  ENST00000523990.1  11.649517  1 6.421920e-04
9888  ENSG00000130779.22 ENST00000302528.11  11.648412  1 6.425735e-04
22256 ENSG00000198720.13  ENST00000394859.8  11.647061  1 6.430403e-04
22257 ENSG00000198720.13  ENST00000487527.5  11.647061  1 6.430403e-04
26837  ENSG00000280739.4  ENST00000629723.2  11.642222  1 6.447155e-04
1084   ENSG00000101846.9  ENST00000674429.1  11.641281  1 6.450417e-04
18275 ENSG00000138757.15  ENST00000677952.1  11.588529  1 6.635989e-04
20623 ENSG00000137288.10  ENST00000606961.1  11.583342  1 6.654524e-04
3895  ENSG00000136717.15 ENST00000316724.10  11.549495  1 6.776767e-04
21453 ENSG00000047634.15  ENST00000380045.7  11.529484  1 6.850103e-04
11344 ENSG00000130349.10  ENST00000625458.1  11.525667  1 6.864183e-04
14383 ENSG00000183032.12  ENST00000331299.6  11.511416  1 6.917005e-04
14384 ENSG00000183032.12  ENST00000555449.5  11.511416  1 6.917005e-04
24927 ENSG00000204934.10  ENST00000488315.5  11.498752  1 6.964293e-04
24926 ENSG00000204934.10  ENST00000461019.5  11.498752  1 6.964293e-04
2758  ENSG00000126759.14  ENST00000485991.5  11.492935  1 6.986123e-04
22313 ENSG00000168175.15  ENST00000395468.9  11.484901  1 7.016388e-04
22314 ENSG00000168175.15  ENST00000622254.1  11.484901  1 7.016388e-04
4307  ENSG00000072310.18  ENST00000355815.8  11.470849  1 7.069638e-04
24028 ENSG00000196922.11  ENST00000427606.2  11.450790  1 7.146361e-04
10629 ENSG00000171552.14  ENST00000376062.6  11.441705  1 7.181386e-04
17464 ENSG00000198208.12  ENST00000557413.6  11.436058  1 7.203245e-04
7944  ENSG00000158186.13  ENST00000289104.8  11.431903  1 7.219372e-04
7945  ENSG00000158186.13  ENST00000423968.7  11.431903  1 7.219372e-04
12947  ENSG00000181291.8  ENST00000321639.7  11.421825  1 7.258635e-04
12948  ENSG00000181291.8  ENST00000631683.2  11.421825  1 7.258635e-04
6677   ENSG00000145375.9  ENST00000274008.5  11.407942  1 7.313081e-04
1101  ENSG00000102081.16  ENST00000690137.1  11.401025  1 7.340360e-04
15263 ENSG00000075420.13  ENST00000416957.5  11.385567  1 7.401695e-04
20278 ENSG00000159214.13  ENST00000372318.8  11.379112  1 7.427463e-04
3634  ENSG00000134982.17  ENST00000257430.9  11.361083  1 7.499909e-04
3635  ENSG00000134982.17  ENST00000508376.6  11.361083  1 7.499909e-04
3946  ENSG00000137177.20  ENST00000378814.9  11.359327  1 7.507002e-04
11258 ENSG00000178821.13  ENST00000310991.8  11.358877  1 7.508822e-04
20716 ENSG00000182667.15  ENST00000683400.1  11.354483  1 7.526606e-04
6905  ENSG00000148019.14  ENST00000424347.6  11.342309  1 7.576109e-04
14036 ENSG00000182511.12  ENST00000328850.8  11.338039  1 7.593545e-04
14037 ENSG00000182511.12  ENST00000414248.6  11.338039  1 7.593545e-04
6924  ENSG00000148396.19 ENST00000313050.11  11.336078  1 7.601569e-04
26332 ENSG00000154217.16  ENST00000581322.6  11.327213  1 7.637944e-04
18450 ENSG00000198265.12 ENST00000358691.10  11.323602  1 7.652813e-04
18451 ENSG00000198265.12  ENST00000580168.5  11.323602  1 7.652813e-04
9611  ENSG00000167524.16 ENST00000301037.11  11.321523  1 7.661384e-04
25208 ENSG00000162086.16  ENST00000617839.1  11.311335  1 7.703537e-04
9413   ENSG00000123575.9  ENST00000299906.5  11.305654  1 7.727141e-04
9414   ENSG00000123575.9  ENST00000493442.2  11.305654  1 7.727141e-04
10331 ENSG00000172059.11  ENST00000305883.6  11.287255  1 7.804098e-04
10332 ENSG00000172059.11  ENST00000540845.5  11.287255  1 7.804098e-04
11104 ENSG00000173933.21  ENST00000396053.9  11.281937  1 7.826484e-04
26652  ENSG00000273136.8  ENST00000609741.2  11.275213  1 7.854886e-04
4401   ENSG00000138593.9  ENST00000559471.6  11.274724  1 7.856952e-04
4400   ENSG00000138593.9  ENST00000261847.7  11.274724  1 7.856952e-04
5435  ENSG00000080709.16  ENST00000673685.1  11.268039  1 7.885298e-04
17074 ENSG00000166833.23  ENST00000360655.8  11.261776  1 7.911946e-04
21626 ENSG00000100416.15  ENST00000476901.1  11.259847  1 7.920173e-04
21627 ENSG00000100416.15  ENST00000645190.1  11.259847  1 7.920173e-04
5625  ENSG00000122515.16  ENST00000413916.5  11.259052  1 7.923566e-04
2389  ENSG00000122218.16  ENST00000241704.8  11.258038  1 7.927898e-04
22287 ENSG00000110031.13  ENST00000528954.5  11.250657  1 7.959485e-04
19012 ENSG00000198925.12  ENST00000396761.6  11.248550  1 7.968526e-04
15161 ENSG00000155506.19  ENST00000690816.1  11.245646  1 7.981003e-04
7014  ENSG00000149269.10  ENST00000356341.8  11.238570  1 8.011487e-04
16337 ENSG00000188313.13  ENST00000448787.6  11.238538  1 8.011626e-04
13606 ENSG00000128699.14  ENST00000392349.9  11.237020  1 8.018181e-04
11373 ENSG00000174796.12  ENST00000311638.7  11.224502  1 8.072442e-04
11374 ENSG00000174796.12  ENST00000507556.5  11.224502  1 8.072442e-04
2711  ENSG00000126070.20  ENST00000373191.9  11.195006  1 8.201776e-04
15163 ENSG00000070476.15  ENST00000389709.8  11.194481  1 8.204098e-04
24770  ENSG00000279170.3  ENST00000623858.2  11.191641  1 8.216663e-04
15162 ENSG00000070476.15  ENST00000336332.5  11.185230  1 8.245105e-04
16185 ENSG00000184992.13  ENST00000672415.1  11.168450  1 8.320009e-04
1866  ENSG00000112715.26  ENST00000372067.8  11.155690  1 8.377433e-04
1868  ENSG00000112715.26  ENST00000425836.8  11.155689  1 8.377436e-04
25421 ENSG00000188848.17  ENST00000504360.5  11.144411  1 8.428524e-04
25420 ENSG00000188848.17  ENST00000502486.6  11.144411  1 8.428524e-04
23223 ENSG00000176124.15  ENST00000469754.3  11.126214  1 8.511613e-04
13436 ENSG00000110931.19  ENST00000404169.8  11.108842  1 8.591713e-04
12854 ENSG00000005436.14  ENST00000409857.7  11.102016  1 8.623393e-04
5455   ENSG00000105088.9  ENST00000264833.9  11.086985  1 8.693571e-04
224    ENSG00000253507.6  ENST00000519005.1  11.073686  1 8.756145e-04
26685  ENSG00000276077.4  ENST00000625096.3  11.067192  1 8.786864e-04
20421 ENSG00000204084.13  ENST00000373024.8  11.042706  1 8.903681e-04
20422 ENSG00000204084.13  ENST00000373027.5  11.042706  1 8.903681e-04
19019 ENSG00000131778.20  ENST00000369259.4  11.025347  1 8.987445e-04
19018 ENSG00000131778.20  ENST00000369258.8  11.025347  1 8.987445e-04
17721 ENSG00000163946.14  ENST00000493960.6  11.025337  1 8.987492e-04
12625 ENSG00000180398.13  ENST00000409913.5  11.023011  1 8.998776e-04
12624 ENSG00000180398.13  ENST00000319466.9  11.023011  1 8.998776e-04
18320 ENSG00000100296.14  ENST00000397871.5  11.019376  1 9.016444e-04
12546 ENSG00000111679.17  ENST00000399448.5  11.011906  1 9.052852e-04
7263  ENSG00000151806.14  ENST00000506793.5  10.993271  1 9.144328e-04
7262  ENSG00000151806.14  ENST00000281543.6  10.993271  1 9.144328e-04
23182 ENSG00000163882.10  ENST00000456318.6  10.988993  1 9.165459e-04
6828  ENSG00000146966.13  ENST00000537639.5  10.978961  1 9.215207e-04
7293   ENSG00000123066.9  ENST00000648737.1  10.978529  1 9.217355e-04
1508  ENSG00000106692.15 ENST00000357998.10  10.978235  1 9.218819e-04
5116  ENSG00000081320.11  ENST00000409228.5  10.967328  1 9.273235e-04
5115  ENSG00000081320.11  ENST00000263955.9  10.967328  1 9.273235e-04
3261  ENSG00000131089.17  ENST00000635729.1  10.950093  1 9.359890e-04
3355  ENSG00000132205.11  ENST00000254528.4  10.937644  1 9.422989e-04
3356  ENSG00000132205.11  ENST00000308080.9  10.937644  1 9.422989e-04
2197  ENSG00000116977.19  ENST00000366584.9  10.935491  1 9.433949e-04
16584  ENSG00000221923.9  ENST00000424032.6  10.934869  1 9.437116e-04
5552  ENSG00000039560.14  ENST00000265109.8  10.934530  1 9.438840e-04
5553  ENSG00000039560.14  ENST00000512629.5  10.934530  1 9.438840e-04
3827  ENSG00000136280.17  ENST00000461377.5  10.928747  1 9.468351e-04
1894  ENSG00000112983.18  ENST00000402931.5  10.905878  1 9.585962e-04
17733 ENSG00000079805.19  ENST00000389253.9  10.893303  1 9.651255e-04
22858 ENSG00000138081.22  ENST00000402508.5  10.891834  1 9.658915e-04
11864 ENSG00000135317.14  ENST00000369627.6  10.889230  1 9.672504e-04
5801  ENSG00000079102.16  ENST00000615601.4  10.884277  1 9.698401e-04
20682 ENSG00000204220.12 ENST00000374606.10  10.881743  1 9.711683e-04
4533  ENSG00000176406.23  ENST00000504942.6  10.874110  1 9.751790e-04
24769  ENSG00000279170.3  ENST00000607332.2  10.869793  1 9.774544e-04
23412 ENSG00000127990.19  ENST00000447873.6  10.837840  1 9.944665e-04
17377 ENSG00000143437.21 ENST00000358595.10  10.830932  1 9.981838e-04
8190  ENSG00000188171.17  ENST00000291750.6  10.809667  1 1.009714e-03
8191  ENSG00000188171.17  ENST00000601440.6  10.809667  1 1.009714e-03
8605  ENSG00000163281.12  ENST00000509756.1  10.804748  1 1.012401e-03
11004 ENSG00000173915.16  ENST00000309579.7  10.803654  1 1.012999e-03
11005 ENSG00000173915.16  ENST00000369815.6  10.803654  1 1.012999e-03
6823  ENSG00000146938.16  ENST00000381093.6  10.802064  1 1.013870e-03
17253 ENSG00000177565.18 ENST00000352800.10  10.798721  1 1.015703e-03
2109  ENSG00000117385.16 ENST00000296388.10  10.791417  1 1.019718e-03
7863  ENSG00000157600.12  ENST00000372073.5  10.784533  1 1.023517e-03
20929 ENSG00000134900.12  ENST00000651448.1  10.748822  1 1.043457e-03
10627 ENSG00000166377.21  ENST00000586722.5  10.744692  1 1.045788e-03
477   ENSG00000061273.18 ENST00000080059.12  10.739931  1 1.048482e-03
18994 ENSG00000198901.14  ENST00000394249.8  10.736393  1 1.050489e-03
3476  ENSG00000133315.12  ENST00000255681.7  10.714458  1 1.063016e-03
3477  ENSG00000133315.12  ENST00000538595.1  10.714458  1 1.063016e-03
21869 ENSG00000138756.19  ENST00000389010.7  10.701209  1 1.070656e-03
21870 ENSG00000138756.19  ENST00000502613.3  10.701209  1 1.070656e-03
6274  ENSG00000141644.18 ENST00000269468.10  10.687211  1 1.078787e-03
9879  ENSG00000121940.17  ENST00000675650.1  10.680623  1 1.082636e-03
13783 ENSG00000157216.16  ENST00000417664.7  10.671995  1 1.087697e-03
6114  ENSG00000140557.12  ENST00000268164.8  10.669221  1 1.089330e-03
21580 ENSG00000205572.10  ENST00000380750.8  10.666436  1 1.090971e-03
14209 ENSG00000162614.19  ENST00000401035.7  10.651582  1 1.099768e-03
22037 ENSG00000177614.11  ENST00000391860.7  10.646444  1 1.102828e-03
22038 ENSG00000177614.11  ENST00000525115.1  10.646444  1 1.102828e-03
23416  ENSG00000234773.8  ENST00000415793.7  10.641297  1 1.105901e-03
23417  ENSG00000234773.8  ENST00000426044.1  10.641297  1 1.105901e-03
26863  ENSG00000280623.1  ENST00000626825.1  10.640202  1 1.106556e-03
11424 ENSG00000175216.15  ENST00000312055.9  10.637544  1 1.108147e-03
22848 ENSG00000186951.17  ENST00000407236.6  10.632089  1 1.111421e-03
22849 ENSG00000186951.17  ENST00000493286.1  10.632089  1 1.111421e-03
2327  ENSG00000121210.16  ENST00000240487.5  10.614577  1 1.121996e-03
4039  ENSG00000137841.12  ENST00000559381.5  10.605492  1 1.127522e-03
22001 ENSG00000141376.23  ENST00000589222.5  10.602856  1 1.129131e-03
19851 ENSG00000116396.15  ENST00000369787.7  10.593881  1 1.134625e-03
5166  ENSG00000077232.19 ENST00000264065.12  10.587390  1 1.138616e-03
21183 ENSG00000147044.23  ENST00000378158.6  10.577652  1 1.144629e-03
17564 ENSG00000133961.21  ENST00000555238.6  10.577650  1 1.144631e-03
18217 ENSG00000197563.11  ENST00000400334.7  10.562053  1 1.154329e-03
10809 ENSG00000048649.14  ENST00000480887.5  10.553522  1 1.159669e-03
10235 ENSG00000140987.21  ENST00000396852.9  10.534165  1 1.171878e-03
20850 ENSG00000076053.12  ENST00000540163.5  10.527642  1 1.176022e-03
3094   ENSG00000243156.9  ENST00000461307.5  10.521354  1 1.180030e-03
4216  ENSG00000121897.15  ENST00000640381.1  10.517898  1 1.182239e-03
16055 ENSG00000164828.18  ENST00000389574.7  10.515844  1 1.183553e-03
25213  ENSG00000245958.7  ENST00000503038.1  10.505131  1 1.190435e-03
7588  ENSG00000154783.12  ENST00000543601.5  10.501920  1 1.192506e-03
15218 ENSG00000181577.16  ENST00000442114.6  10.485576  1 1.203101e-03
22980 ENSG00000064547.14  ENST00000407877.8  10.481701  1 1.205627e-03
22981 ENSG00000064547.14  ENST00000542587.5  10.481701  1 1.205627e-03
20851 ENSG00000076053.12  ENST00000542140.5  10.468944  1 1.213981e-03
11239 ENSG00000173226.17 ENST00000310864.11  10.466985  1 1.215269e-03
26705  ENSG00000274265.5  ENST00000667654.1  10.456167  1 1.222407e-03
26706  ENSG00000274265.5  ENST00000668239.1  10.456167  1 1.222407e-03
20687 ENSG00000133216.17  ENST00000400191.7  10.436715  1 1.235348e-03
3499  ENSG00000133703.14 ENST00000256078.10  10.429009  1 1.240513e-03
3500  ENSG00000133703.14  ENST00000311936.8  10.429009  1 1.240513e-03
20386 ENSG00000024048.11  ENST00000372899.6  10.426686  1 1.242074e-03
20387 ENSG00000024048.11  ENST00000372901.2  10.426686  1 1.242074e-03
10023 ENSG00000169057.24 ENST00000303391.11  10.418188  1 1.247803e-03
10489 ENSG00000169727.13  ENST00000578552.6  10.417762  1 1.248091e-03
13    ENSG00000111186.13  ENST00000397196.7  10.393995  1 1.264258e-03
9996  ENSG00000172071.15  ENST00000684455.1  10.383436  1 1.271509e-03
5698  ENSG00000114770.17 ENST00000265586.10  10.377626  1 1.275516e-03
22062 ENSG00000141526.18  ENST00000584689.6  10.368631  1 1.281746e-03
22061 ENSG00000141526.18  ENST00000582743.6  10.368631  1 1.281746e-03
6534  ENSG00000118257.17  ENST00000360409.7  10.350578  1 1.294341e-03
18273 ENSG00000138757.15  ENST00000357854.7  10.350245  1 1.294575e-03
12627 ENSG00000141447.19  ENST00000357041.8  10.335124  1 1.305223e-03
12872 ENSG00000010244.19 ENST00000321233.10  10.324826  1 1.312526e-03
12797 ENSG00000186187.12  ENST00000568844.1  10.319277  1 1.316479e-03
11268 ENSG00000172687.14  ENST00000311015.7  10.299305  1 1.330803e-03
5673  ENSG00000124920.14  ENST00000675792.1  10.294553  1 1.334235e-03
3070  ENSG00000100364.19  ENST00000391627.6  10.290900  1 1.336879e-03
169   ENSG00000164093.18  ENST00000644743.1  10.285359  1 1.340899e-03
16812 ENSG00000090989.18  ENST00000381295.7  10.282924  1 1.342670e-03
12044 ENSG00000114779.20  ENST00000395008.6  10.282533  1 1.342955e-03
895   ENSG00000100105.18  ENST00000215919.3  10.274479  1 1.348829e-03
1822  ENSG00000112062.11  ENST00000229794.9  10.271943  1 1.350685e-03
1823  ENSG00000112062.11  ENST00000229795.7  10.271943  1 1.350685e-03
15867 ENSG00000148498.16  ENST00000374789.8  10.261340  1 1.358470e-03
21021 ENSG00000105357.20  ENST00000376970.6  10.247158  1 1.368954e-03
21022 ENSG00000105357.20  ENST00000425460.6  10.247158  1 1.368954e-03
19015 ENSG00000170776.22  ENST00000394518.7  10.245068  1 1.370505e-03
19014 ENSG00000170776.22  ENST00000394510.6  10.245068  1 1.370505e-03
6619  ENSG00000144908.14  ENST00000476245.5  10.242820  1 1.372177e-03
18966 ENSG00000132698.15 ENST00000361084.10  10.226356  1 1.384479e-03
19078 ENSG00000198771.11  ENST00000367854.8  10.212252  1 1.395107e-03
19079 ENSG00000198771.11  ENST00000537350.5  10.212252  1 1.395107e-03
22942 ENSG00000164199.18  ENST00000640815.1  10.209770  1 1.396986e-03
20377 ENSG00000241343.10  ENST00000471855.1  10.208801  1 1.397720e-03
16364 ENSG00000124104.19  ENST00000372542.5  10.205600  1 1.400148e-03
10093 ENSG00000169621.10  ENST00000303795.9  10.204486  1 1.400995e-03
10094 ENSG00000169621.10  ENST00000529851.5  10.204486  1 1.400995e-03
4247  ENSG00000092020.11  ENST00000557278.1  10.200795  1 1.403802e-03
10285  ENSG00000169217.9  ENST00000305596.8  10.192713  1 1.409967e-03
10286  ENSG00000169217.9  ENST00000569466.1  10.192713  1 1.409967e-03
11240 ENSG00000173226.17 ENST00000349820.10  10.178031  1 1.421238e-03
6580  ENSG00000144713.13  ENST00000457131.1  10.176964  1 1.422061e-03
21333  ENSG00000288558.2  ENST00000673665.1  10.168512  1 1.428595e-03
11516 ENSG00000109956.13  ENST00000392580.5  10.143817  1 1.447860e-03
20937 ENSG00000204498.11  ENST00000376146.8  10.130646  1 1.458243e-03
2934  ENSG00000129351.17  ENST00000590261.5  10.130221  1 1.458579e-03
18469 ENSG00000126804.14  ENST00000554015.5  10.093945  1 1.487573e-03
2837  ENSG00000127863.16  ENST00000382263.3  10.090790  1 1.490122e-03
2836  ENSG00000127863.16  ENST00000248484.9  10.090790  1 1.490122e-03
10511 ENSG00000172262.12  ENST00000682664.1  10.086840  1 1.493320e-03
16357 ENSG00000188735.13 ENST00000342607.10  10.076239  1 1.501936e-03
16358 ENSG00000188735.13  ENST00000449592.7  10.076239  1 1.501936e-03
23346 ENSG00000177640.16  ENST00000454781.6  10.065647  1 1.510595e-03
23347 ENSG00000177640.16  ENST00000454857.6  10.065647  1 1.510595e-03
7587  ENSG00000154783.12 ENST00000285046.10  10.059520  1 1.515627e-03
11272 ENSG00000110514.19  ENST00000395344.7  10.057264  1 1.517484e-03
6642  ENSG00000145087.13  ENST00000471454.6  10.056901  1 1.517783e-03
6643  ENSG00000145087.13  ENST00000472879.5  10.056901  1 1.517783e-03
8184  ENSG00000160310.19  ENST00000355680.8  10.046824  1 1.526108e-03
4381  ENSG00000113712.19  ENST00000377843.8  10.039649  1 1.532064e-03
6855  ENSG00000125351.13  ENST00000276201.7  10.038304  1 1.533183e-03
6856  ENSG00000125351.13  ENST00000345865.6  10.038304  1 1.533183e-03
3902  ENSG00000136718.10  ENST00000460766.5  10.032994  1 1.537609e-03
9174  ENSG00000102290.23  ENST00000682573.1  10.030147  1 1.539988e-03
5176  ENSG00000114956.20  ENST00000629438.2  10.017732  1 1.550403e-03
21446 ENSG00000132256.20  ENST00000380034.8  10.016484  1 1.551454e-03
10468 ENSG00000169689.15  ENST00000580435.5  10.000712  1 1.564797e-03
10827 ENSG00000160072.20  ENST00000673477.1   9.998059  1 1.567053e-03
14123 ENSG00000185261.15  ENST00000682413.1   9.987243  1 1.576285e-03
23701 ENSG00000139428.12  ENST00000545712.7   9.982375  1 1.580457e-03
3315  ENSG00000131759.18  ENST00000394089.6   9.975521  1 1.586351e-03
16929 ENSG00000116698.22  ENST00000688051.1   9.975148  1 1.586673e-03
10183 ENSG00000168958.20  ENST00000409565.5   9.974204  1 1.587486e-03
17722 ENSG00000163946.14  ENST00000683822.1   9.971989  1 1.589397e-03
14217 ENSG00000182054.10  ENST00000330062.8   9.936282  1 1.620525e-03
16217 ENSG00000073712.15  ENST00000341590.8   9.928432  1 1.627451e-03
9244   ENSG00000165943.5  ENST00000298894.5   9.922695  1 1.632531e-03
9245   ENSG00000165943.5  ENST00000556883.1   9.922695  1 1.632531e-03
19659 ENSG00000188643.11  ENST00000368705.2   9.911153  1 1.642802e-03
24154  ENSG00000227398.5  ENST00000689153.1   9.895475  1 1.656856e-03
19511 ENSG00000120370.14  ENST00000688688.1   9.890940  1 1.660945e-03
12585 ENSG00000116212.15  ENST00000319223.8   9.887100  1 1.664415e-03
12586 ENSG00000116212.15  ENST00000371370.8   9.887100  1 1.664415e-03
5054  ENSG00000129810.15  ENST00000442720.5   9.883081  1 1.668054e-03
4331  ENSG00000072415.10  ENST00000678380.1   9.878232  1 1.672455e-03
14207 ENSG00000162614.19 ENST00000330010.12   9.873883  1 1.676413e-03
12131 ENSG00000120885.22  ENST00000522098.1   9.873481  1 1.676780e-03
2520  ENSG00000124140.15  ENST00000628272.1   9.873204  1 1.677032e-03
16001 ENSG00000185630.19  ENST00000420696.7   9.865345  1 1.684211e-03
21894 ENSG00000204842.18  ENST00000673436.1   9.865286  1 1.684265e-03
24125  ENSG00000226824.8  ENST00000693151.1   9.860926  1 1.688261e-03
26333  ENSG00000263412.2  ENST00000578660.1   9.855111  1 1.693606e-03
18091 ENSG00000173209.23  ENST00000471542.5   9.854714  1 1.693971e-03
3115   ENSG00000130035.9  ENST00000252318.7   9.851548  1 1.696889e-03
17414 ENSG00000197859.11  ENST00000393060.1   9.832906  1 1.714173e-03
17415 ENSG00000197859.11  ENST00000651351.2   9.832906  1 1.714173e-03
15768 ENSG00000189171.15  ENST00000476133.6   9.817854  1 1.728259e-03
7884  ENSG00000148219.18  ENST00000373986.7   9.815153  1 1.730799e-03
12961  ENSG00000185015.8  ENST00000321764.4   9.814262  1 1.731638e-03
12962  ENSG00000185015.8  ENST00000522631.1   9.814262  1 1.731638e-03
22917 ENSG00000105889.16  ENST00000424363.5   9.811143  1 1.734577e-03
22392 ENSG00000100167.21  ENST00000396426.7   9.808479  1 1.737091e-03
12061 ENSG00000107957.17  ENST00000369774.9   9.795377  1 1.749512e-03
9422  ENSG00000166750.10  ENST00000299977.9   9.795307  1 1.749578e-03
9423  ENSG00000166750.10  ENST00000542451.1   9.795307  1 1.749578e-03
16971 ENSG00000141198.16  ENST00000575882.6   9.794391  1 1.750450e-03
4845  ENSG00000123240.17  ENST00000263036.9   9.793129  1 1.751651e-03
22729 ENSG00000008513.16  ENST00000521180.5   9.780423  1 1.763798e-03
22730 ENSG00000008513.16  ENST00000522652.6   9.780423  1 1.763798e-03
25977  ENSG00000257621.9  ENST00000654187.2   9.778110  1 1.766018e-03
18754 ENSG00000137486.17  ENST00000360025.7   9.777108  1 1.766980e-03
18755 ENSG00000137486.17  ENST00000420843.7   9.777108  1 1.766980e-03
20379 ENSG00000241343.10  ENST00000614077.4   9.771201  1 1.772666e-03
26774  ENSG00000277067.4  ENST00000623095.3   9.746895  1 1.796259e-03
23273 ENSG00000206337.12  ENST00000414046.3   9.735052  1 1.807869e-03
23274 ENSG00000206337.12  ENST00000670109.1   9.735052  1 1.807869e-03
17168 ENSG00000122756.15  ENST00000610543.4   9.731289  1 1.811574e-03
18708 ENSG00000197056.11  ENST00000488455.5   9.729082  1 1.813751e-03
13294 ENSG00000108515.18  ENST00000522301.5   9.707362  1 1.835313e-03
24800 ENSG00000146556.15  ENST00000692602.1   9.689641  1 1.853097e-03
19069 ENSG00000198718.13  ENST00000361577.7   9.686853  1 1.855912e-03
12241 ENSG00000147548.17  ENST00000316985.7   9.678180  1 1.864692e-03
12242 ENSG00000147548.17 ENST00000317025.13   9.678180  1 1.864692e-03
7756  ENSG00000156650.14 ENST00000287239.10   9.669810  1 1.873207e-03
5040  ENSG00000116353.16  ENST00000373791.7   9.666602  1 1.876480e-03
1020  ENSG00000100908.14  ENST00000419198.6   9.665389  1 1.877720e-03
19832  ENSG00000146242.9  ENST00000369750.4   9.664597  1 1.878530e-03
19833  ENSG00000146242.9  ENST00000543496.3   9.664597  1 1.878530e-03
7942  ENSG00000158169.13  ENST00000289081.8   9.656077  1 1.887262e-03
7943  ENSG00000158169.13  ENST00000375305.6   9.656077  1 1.887262e-03
13240 ENSG00000103051.20  ENST00000530314.5   9.648777  1 1.894777e-03
13239 ENSG00000103051.20 ENST00000323786.10   9.648777  1 1.894777e-03
12853 ENSG00000005436.14  ENST00000321027.8   9.641561  1 1.902236e-03
20922 ENSG00000171729.14  ENST00000428417.5   9.623524  1 1.921008e-03
16312 ENSG00000135540.12 ENST00000343505.10   9.618994  1 1.925752e-03
16313 ENSG00000135540.12  ENST00000427025.6   9.618994  1 1.925752e-03
6882  ENSG00000147601.15 ENST00000276603.10   9.618091  1 1.926699e-03
13788 ENSG00000176155.20  ENST00000389641.9   9.614264  1 1.930718e-03
17813 ENSG00000197321.16  ENST00000674475.1   9.614250  1 1.930733e-03
11061 ENSG00000003402.21 ENST00000341222.10   9.602117  1 1.943532e-03
15722  ENSG00000180008.9  ENST00000555846.2   9.600736  1 1.944994e-03
15721  ENSG00000180008.9  ENST00000395472.2   9.600736  1 1.944994e-03
8506  ENSG00000162714.13  ENST00000294753.8   9.599802  1 1.945983e-03
6072  ENSG00000140416.23 ENST00000267996.11   9.589854  1 1.956555e-03
6073  ENSG00000140416.23  ENST00000358278.7   9.589854  1 1.956555e-03
11865 ENSG00000135317.14  ENST00000505648.5   9.587137  1 1.959453e-03
8407  ENSG00000005513.10  ENST00000293894.4   9.582389  1 1.964526e-03
8408  ENSG00000005513.10  ENST00000566034.1   9.582389  1 1.964526e-03
12822 ENSG00000153071.15 ENST00000320816.11   9.579927  1 1.967163e-03
12823 ENSG00000153071.15  ENST00000545653.5   9.579927  1 1.967163e-03
16797 ENSG00000104497.15  ENST00000396330.6   9.573663  1 1.973885e-03
15715 ENSG00000164056.11  ENST00000622283.1   9.573289  1 1.974287e-03
18876 ENSG00000111237.19  ENST00000549970.5   9.572666  1 1.974957e-03
3898  ENSG00000136717.15  ENST00000462958.5   9.565575  1 1.982601e-03
21001 ENSG00000106772.19  ENST00000443509.6   9.564238  1 1.984045e-03
15181 ENSG00000157823.17  ENST00000558011.5   9.551560  1 1.997796e-03
14839 ENSG00000184470.21  ENST00000400521.7   9.546452  1 2.003363e-03
376   ENSG00000017797.13  ENST00000019317.8   9.543866  1 2.006187e-03
377   ENSG00000017797.13  ENST00000383432.8   9.543866  1 2.006187e-03
7586  ENSG00000167306.20  ENST00000592688.1   9.543662  1 2.006411e-03
15471 ENSG00000126970.16  ENST00000337990.2   9.535064  1 2.015832e-03
19836 ENSG00000121931.16  ENST00000369763.5   9.518168  1 2.034476e-03
19837 ENSG00000121931.16  ENST00000485275.2   9.518168  1 2.034476e-03
15144 ENSG00000140382.15  ENST00000336216.9   9.510384  1 2.043124e-03
15145 ENSG00000140382.15  ENST00000381714.7   9.510384  1 2.043124e-03
21858 ENSG00000106133.18  ENST00000485741.6   9.505360  1 2.048726e-03
2039  ENSG00000115486.13  ENST00000687995.1   9.496461  1 2.058686e-03
17255 ENSG00000177565.18  ENST00000673974.1   9.479112  1 2.078245e-03
4986  ENSG00000084234.18  ENST00000263574.9   9.467448  1 2.091501e-03
17735 ENSG00000079805.19  ENST00000585892.5   9.464401  1 2.094978e-03
26653  ENSG00000273136.8  ENST00000619748.4   9.459774  1 2.100269e-03
24712 ENSG00000178971.16  ENST00000643543.1   9.456328  1 2.104219e-03
24430 ENSG00000188828.13  ENST00000674243.1   9.456182  1 2.104386e-03
24429 ENSG00000188828.13  ENST00000480725.2   9.456182  1 2.104386e-03
23194 ENSG00000013374.17  ENST00000413040.7   9.455272  1 2.105431e-03
2253  ENSG00000119950.21  ENST00000652323.1   9.447103  1 2.114829e-03
4174  ENSG00000101670.12  ENST00000623277.1   9.425320  1 2.140098e-03
1649  ENSG00000109794.14  ENST00000227065.8   9.413267  1 2.154211e-03
9883  ENSG00000109919.10  ENST00000534074.5   9.406696  1 2.161945e-03
11522 ENSG00000112763.17  ENST00000541522.5   9.406153  1 2.162584e-03
16768 ENSG00000095787.24  ENST00000420266.6   9.405754  1 2.163055e-03
8576  ENSG00000163093.12  ENST00000392663.6   9.404125  1 2.164978e-03
13502 ENSG00000105443.16  ENST00000391881.7   9.396302  1 2.174236e-03
8373  ENSG00000197283.18  ENST00000682587.1   9.393578  1 2.177469e-03
14139 ENSG00000072736.19  ENST00000329524.8   9.392571  1 2.178665e-03
20683 ENSG00000204220.12  ENST00000374607.5   9.388974  1 2.182944e-03
19013 ENSG00000198925.12  ENST00000409618.5   9.368539  1 2.207414e-03
2200  ENSG00000119321.10  ENST00000685945.1   9.357110  1 2.221221e-03
14476 ENSG00000065357.20  ENST00000394147.5   9.350595  1 2.229131e-03
14475 ENSG00000065357.20 ENST00000331886.10   9.350595  1 2.229131e-03
14593 ENSG00000185909.15  ENST00000332780.4   9.348068  1 2.232207e-03
14594 ENSG00000185909.15  ENST00000462582.1   9.348068  1 2.232207e-03
11515 ENSG00000109956.13  ENST00000312527.9   9.343319  1 2.237999e-03
1671  ENSG00000109944.11  ENST00000227349.7   9.322009  1 2.264176e-03
4672  ENSG00000089091.16  ENST00000262547.9   9.320457  1 2.266095e-03
6800  ENSG00000112531.17  ENST00000361758.8   9.311847  1 2.276769e-03
13293 ENSG00000108515.18  ENST00000521659.5   9.296765  1 2.295588e-03
17718 ENSG00000107560.12  ENST00000355624.8   9.280586  1 2.315953e-03
17719 ENSG00000107560.12  ENST00000369199.5   9.280586  1 2.315953e-03
18998 ENSG00000198728.11  ENST00000673968.1   9.279293  1 2.317588e-03
10244 ENSG00000106400.12  ENST00000305105.3   9.279005  1 2.317953e-03
12905 ENSG00000013441.17  ENST00000321356.9   9.272349  1 2.326391e-03
19037 ENSG00000110002.16  ENST00000361352.9   9.272100  1 2.326707e-03
17854 ENSG00000019144.20  ENST00000534140.2   9.270694  1 2.328495e-03
13263 ENSG00000173818.17  ENST00000518137.6   9.266099  1 2.334344e-03
8480  ENSG00000162642.14  ENST00000294661.8   9.263347  1 2.337854e-03
1534  ENSG00000107771.17 ENST00000224756.12   9.262991  1 2.338308e-03
3507  ENSG00000133731.10  ENST00000449740.6   9.260094  1 2.342010e-03
45     ENSG00000103121.9         BambuTx132   9.246992  1 2.358826e-03
21735 ENSG00000104723.21  ENST00000382020.8   9.242699  1 2.364362e-03
7337   ENSG00000251201.8  ENST00000282382.8   9.226145  1 2.385835e-03
7338   ENSG00000251201.8  ENST00000333314.3   9.226145  1 2.385835e-03
6824  ENSG00000146938.16  ENST00000381095.8   9.224899  1 2.387459e-03
7785  ENSG00000156931.16  ENST00000436792.6   9.224617  1 2.387826e-03
7784  ENSG00000156931.16  ENST00000287546.8   9.224617  1 2.387826e-03
16723 ENSG00000181852.18  ENST00000345093.9   9.223972  1 2.388667e-03
20902  ENSG00000263020.6  ENST00000375880.6   9.219288  1 2.394786e-03
6449  ENSG00000143554.14  ENST00000624995.4   9.218864  1 2.395342e-03
15573 ENSG00000153130.18  ENST00000338517.8   9.218305  1 2.396073e-03
4128  ENSG00000070961.16  ENST00000428670.8   9.211928  1 2.404433e-03
2091  ENSG00000116670.15  ENST00000376667.7   9.207401  1 2.410387e-03
2092  ENSG00000116670.15  ENST00000376692.9   9.207401  1 2.410387e-03
22018  ENSG00000178935.5  ENST00000596248.1   9.200326  1 2.419721e-03
22017  ENSG00000178935.5  ENST00000391701.1   9.200326  1 2.419721e-03
12628 ENSG00000141447.19  ENST00000399443.7   9.193500  1 2.428760e-03
26393  ENSG00000267383.8  ENST00000592022.1   9.193218  1 2.429134e-03
26392  ENSG00000267383.8  ENST00000585816.1   9.193218  1 2.429134e-03
9952  ENSG00000132535.22  ENST00000489885.1   9.191849  1 2.430952e-03
1008  ENSG00000100836.11  ENST00000397276.6   9.178477  1 2.448778e-03
1007  ENSG00000100836.11  ENST00000216727.9   9.178477  1 2.448778e-03
17812 ENSG00000197321.16  ENST00000375400.7   9.170876  1 2.458968e-03
9129  ENSG00000148187.18  ENST00000373729.5   9.166133  1 2.465349e-03
12302 ENSG00000100280.17  ENST00000405198.6   9.157008  1 2.477674e-03
12303 ENSG00000100280.17  ENST00000432560.6   9.155674  1 2.479480e-03
15282 ENSG00000145335.17  ENST00000394991.8   9.152158  1 2.484249e-03
6683  ENSG00000145390.12  ENST00000692078.1   9.146993  1 2.491271e-03
19301 ENSG00000168275.16  ENST00000366613.1   9.146987  1 2.491279e-03
19302 ENSG00000168275.16  ENST00000619305.1   9.146987  1 2.491279e-03
19765 ENSG00000132424.17  ENST00000460600.1   9.144387  1 2.494822e-03
14981 ENSG00000176473.14 ENST00000335290.10   9.142848  1 2.496922e-03
15342 ENSG00000083312.19  ENST00000506351.6   9.114580  1 2.535802e-03
21959 ENSG00000146267.12  ENST00000480148.1   9.110185  1 2.541901e-03
3416  ENSG00000132604.11  ENST00000254942.8   9.100685  1 2.555138e-03
3417  ENSG00000132604.11  ENST00000569584.6   9.100685  1 2.555138e-03
20435 ENSG00000163873.10  ENST00000373091.8   9.065536  1 2.604722e-03
20436 ENSG00000163873.10  ENST00000373093.4   9.065536  1 2.604722e-03
5442  ENSG00000071127.17  ENST00000499869.7   9.054087  1 2.621082e-03
5441  ENSG00000071127.17  ENST00000382452.6   9.054087  1 2.621082e-03
16528 ENSG00000181450.18 ENST00000343776.10   9.046754  1 2.631617e-03
16529 ENSG00000181450.18  ENST00000397097.4   9.046754  1 2.631617e-03
8150  ENSG00000160191.18 ENST00000291539.11   9.042878  1 2.637202e-03
8151  ENSG00000160191.18  ENST00000335512.8   9.042878  1 2.637202e-03
15447 ENSG00000142599.19  ENST00000377464.5   9.036829  1 2.645942e-03
23323 ENSG00000162923.17  ENST00000678555.1   9.035807  1 2.647422e-03
23322 ENSG00000162923.17  ENST00000651911.2   9.035807  1 2.647422e-03
4443  ENSG00000037280.16  ENST00000393347.7   9.033175  1 2.651235e-03
4442  ENSG00000037280.16 ENST00000261937.11   9.033175  1 2.651235e-03
3709  ENSG00000115317.12  ENST00000258080.8   9.030999  1 2.654393e-03
25409 ENSG00000146067.16  ENST00000510479.5   9.024947  1 2.663196e-03
8195  ENSG00000105227.16  ENST00000324001.8   9.020590  1 2.669553e-03
15599 ENSG00000116288.13 ENST00000338639.10   9.015945  1 2.676344e-03
12753 ENSG00000106462.12  ENST00000350995.6   9.006579  1 2.690095e-03
8745  ENSG00000163697.17  ENST00000513611.5   9.006519  1 2.690184e-03
15156 ENSG00000131748.16  ENST00000394250.8   9.001631  1 2.697388e-03
17248 ENSG00000128585.18 ENST00000352689.11   9.000485  1 2.699079e-03
6978   ENSG00000148948.8  ENST00000528697.6   8.982051  1 2.726445e-03
17740 ENSG00000187239.17  ENST00000446176.7   8.978089  1 2.732363e-03
10028 ENSG00000170638.10  ENST00000303434.8   8.976870  1 2.734186e-03
5      ENSG00000256591.5  ENST00000536670.5   8.976249  1 2.735116e-03
13448 ENSG00000221988.13 ENST00000324816.11   8.973841  1 2.738723e-03
9609  ENSG00000109103.12  ENST00000470125.5   8.972812  1 2.740266e-03
1959  ENSG00000114857.19 ENST00000232978.13   8.967843  1 2.747728e-03
1960  ENSG00000114857.19  ENST00000429888.5   8.967843  1 2.747728e-03
25516 ENSG00000249859.13  ENST00000653522.1   8.961440  1 2.757375e-03
11669 ENSG00000168395.16 ENST00000313552.11   8.960526  1 2.758755e-03
11670 ENSG00000168395.16  ENST00000636051.1   8.960526  1 2.758755e-03
663   ENSG00000079156.17  ENST00000409045.7   8.948353  1 2.777198e-03
7235  ENSG00000151491.14  ENST00000647224.1   8.945626  1 2.781347e-03
16950 ENSG00000003756.17  ENST00000347869.8   8.926481  1 2.810653e-03
11063 ENSG00000003402.21  ENST00000423241.6   8.924514  1 2.813682e-03
14157 ENSG00000184809.13  ENST00000380604.8   8.919257  1 2.821792e-03
11901 ENSG00000110497.15  ENST00000534300.5   8.918886  1 2.822366e-03
5168  ENSG00000077232.19  ENST00000616986.5   8.917455  1 2.824578e-03
22972 ENSG00000204406.14  ENST00000638043.2   8.903895  1 2.845630e-03
15618 ENSG00000182568.17  ENST00000454909.6   8.900516  1 2.850901e-03
24701 ENSG00000183666.18  ENST00000691699.1   8.882002  1 2.879956e-03
21796 ENSG00000134490.14  ENST00000383233.8   8.878187  1 2.885980e-03
13011  ENSG00000177700.6  ENST00000322028.5   8.875163  1 2.890764e-03
13012  ENSG00000177700.6  ENST00000534030.1   8.875163  1 2.890764e-03
17674 ENSG00000198055.11  ENST00000355958.9   8.872626  1 2.894784e-03
12550 ENSG00000137343.18 ENST00000318999.11   8.870962  1 2.897424e-03
13472 ENSG00000158560.14  ENST00000359388.8   8.865729  1 2.905741e-03
18150 ENSG00000005810.19 ENST00000357337.11   8.859711  1 2.915338e-03
21399 ENSG00000124786.12  ENST00000648987.1   8.852532  1 2.926826e-03
3250  ENSG00000131016.17  ENST00000359755.5   8.849706  1 2.931361e-03
4135  ENSG00000091039.17  ENST00000393249.6   8.838406  1 2.949567e-03
18344 ENSG00000197694.18  ENST00000372739.7   8.835573  1 2.954149e-03
2654  ENSG00000125744.12  ENST00000430715.6   8.835039  1 2.955012e-03
22609  ENSG00000253846.3  ENST00000612503.1   8.832182  1 2.959644e-03
22608  ENSG00000253846.3  ENST00000398610.3   8.832182  1 2.959644e-03
5050  ENSG00000129810.15  ENST00000263753.8   8.823958  1 2.973012e-03
17132 ENSG00000143612.21 ENST00000368521.10   8.800514  1 3.011457e-03
23216  ENSG00000224032.8  ENST00000688370.1   8.797361  1 3.016666e-03
4468  ENSG00000050426.16  ENST00000623495.1   8.795010  1 3.020556e-03
16706 ENSG00000188732.11  ENST00000409653.5   8.791454  1 3.026450e-03
14778 ENSG00000094631.21 ENST00000334136.11   8.789190  1 3.030208e-03
14779 ENSG00000094631.21  ENST00000644068.1   8.789190  1 3.030208e-03
6151  ENSG00000140990.15 ENST00000268668.11   8.785849  1 3.035762e-03
3262  ENSG00000131089.17  ENST00000671741.2   8.784343  1 3.038269e-03
952   ENSG00000100425.19  ENST00000404034.5   8.780074  1 3.045389e-03
953   ENSG00000100425.19  ENST00000404760.6   8.780074  1 3.045389e-03
16803 ENSG00000120899.18 ENST00000346049.10   8.774755  1 3.054283e-03
16804 ENSG00000120899.18  ENST00000397501.5   8.774755  1 3.054283e-03
21492 ENSG00000168994.14  ENST00000380277.6   8.774396  1 3.054883e-03
21493 ENSG00000168994.14  ENST00000380283.5   8.774396  1 3.054883e-03
11917 ENSG00000164306.11 ENST00000314970.11   8.773145  1 3.056978e-03
18663 ENSG00000140511.12  ENST00000359595.8   8.768662  1 3.064501e-03
18664 ENSG00000140511.12  ENST00000558770.5   8.768662  1 3.064501e-03
23562 ENSG00000213988.11  ENST00000418063.3   8.766507  1 3.068124e-03
3566  ENSG00000134245.18  ENST00000369686.9   8.748763  1 3.098121e-03
25615 ENSG00000196951.12  ENST00000664103.1   8.742640  1 3.108541e-03
15819 ENSG00000166348.20  ENST00000418501.5   8.732948  1 3.125109e-03
24906 ENSG00000135253.16  ENST00000610776.5   8.732079  1 3.126598e-03
18008 ENSG00000196531.14  ENST00000678376.1   8.731530  1 3.127539e-03
17474 ENSG00000129007.16  ENST00000395463.3   8.730318  1 3.129620e-03
3897  ENSG00000136717.15  ENST00000409400.1   8.727832  1 3.133888e-03
10233  ENSG00000168672.4  ENST00000304916.4   8.715625  1 3.154943e-03
10234  ENSG00000168672.4  ENST00000652209.1   8.715625  1 3.154943e-03
9684  ENSG00000167703.15  ENST00000412517.3   8.708225  1 3.167774e-03
18733 ENSG00000196562.15  ENST00000495544.5   8.702738  1 3.177324e-03
18734 ENSG00000196562.15  ENST00000688720.1   8.702738  1 3.177324e-03
22860 ENSG00000138081.22  ENST00000493962.6   8.700002  1 3.182096e-03
9202  ENSG00000165689.17 ENST00000298537.11   8.699410  1 3.183131e-03
5935  ENSG00000072041.18 ENST00000266682.10   8.699050  1 3.183759e-03
7892  ENSG00000157764.14  ENST00000496384.7   8.690207  1 3.199243e-03
7893  ENSG00000157764.14  ENST00000642228.1   8.690207  1 3.199243e-03
353   ENSG00000010818.10  ENST00000367603.8   8.680831  1 3.215743e-03
354   ENSG00000010818.10  ENST00000367604.6   8.680831  1 3.215743e-03
18185 ENSG00000196843.17  ENST00000357485.8   8.672433  1 3.230595e-03
18186 ENSG00000196843.17  ENST00000412735.5   8.672433  1 3.230595e-03
20855 ENSG00000095739.11  ENST00000375533.6   8.670763  1 3.233557e-03
20856 ENSG00000095739.11  ENST00000497699.1   8.670763  1 3.233557e-03
13605 ENSG00000128699.14  ENST00000325795.7   8.667751  1 3.238907e-03
11190 ENSG00000172992.13  ENST00000452796.7   8.660622  1 3.251602e-03
13933 ENSG00000174010.10  ENST00000689334.1   8.651477  1 3.267964e-03
17662 ENSG00000198270.13  ENST00000437003.3   8.641127  1 3.286581e-03
3098  ENSG00000100056.12 ENST00000252137.11   8.639051  1 3.290328e-03
17055 ENSG00000126012.13  ENST00000404049.7   8.636311  1 3.295280e-03
9941  ENSG00000108312.15  ENST00000529383.5   8.635474  1 3.296794e-03
16974 ENSG00000119139.21  ENST00000650084.1   8.631088  1 3.304742e-03
9700  ENSG00000161551.15  ENST00000640955.1   8.629034  1 3.308469e-03
6451  ENSG00000143569.19 ENST00000343815.10   8.627448  1 3.311351e-03
2222   ENSG00000119640.9  ENST00000555135.1   8.625221  1 3.315402e-03
1099  ENSG00000102081.16  ENST00000370477.5   8.609725  1 3.343728e-03
5714  ENSG00000104691.16  ENST00000380154.9   8.591840  1 3.376726e-03
5713  ENSG00000104691.16 ENST00000265616.10   8.591840  1 3.376726e-03
17572 ENSG00000179454.14  ENST00000355081.3   8.585779  1 3.387984e-03
17573 ENSG00000179454.14  ENST00000396128.9   8.585779  1 3.387984e-03
4894  ENSG00000099889.14  ENST00000406522.5   8.570767  1 3.416032e-03
21317 ENSG00000105672.15  ENST00000403402.1   8.562115  1 3.432304e-03
23335 ENSG00000144426.19  ENST00000683650.1   8.561092  1 3.434234e-03
20225 ENSG00000173269.14 ENST00000372027.10   8.545749  1 3.463300e-03
20226 ENSG00000173269.14  ENST00000474994.2   8.545749  1 3.463300e-03
15574 ENSG00000153130.18  ENST00000506597.2   8.545295  1 3.464165e-03
3574  ENSG00000134285.11  ENST00000551694.5   8.544329  1 3.466004e-03
3178   ENSG00000169955.8  ENST00000252799.3   8.542212  1 3.470036e-03
17177 ENSG00000169062.15  ENST00000351487.5   8.538363  1 3.477383e-03
14141 ENSG00000072736.19  ENST00000349223.9   8.536130  1 3.481651e-03
23508  ENSG00000244625.7  ENST00000435162.5   8.529770  1 3.493839e-03
18318 ENSG00000196730.13  ENST00000408954.8   8.513541  1 3.525134e-03
18319 ENSG00000196730.13  ENST00000472284.5   8.513541  1 3.525134e-03
23563 ENSG00000213988.11  ENST00000469078.5   8.510144  1 3.531720e-03
5192  ENSG00000058085.15  ENST00000264144.5   8.508282  1 3.535336e-03
5193  ENSG00000058085.15  ENST00000493293.5   8.508282  1 3.535336e-03
2394  ENSG00000122218.16  ENST00000650154.1   8.493664  1 3.563855e-03
23164 ENSG00000232677.10  ENST00000591372.3   8.493191  1 3.564781e-03
11521 ENSG00000112763.17  ENST00000429381.5   8.489348  1 3.572319e-03
19815 ENSG00000064703.13  ENST00000369702.5   8.488964  1 3.573072e-03
19156 ENSG00000169851.15  ENST00000543491.2   8.477065  1 3.596518e-03
24931 ENSG00000175697.11  ENST00000464295.6   8.471998  1 3.606551e-03
9246  ENSG00000011114.15  ENST00000298896.7   8.471617  1 3.607305e-03
6598  ENSG00000144840.10  ENST00000473654.5   8.463709  1 3.623024e-03
        adj_pvalue
20181 8.966705e-61
20182 8.966705e-61
13318 3.386678e-37
10876 1.300533e-32
10877 1.300533e-32
11418 1.411698e-31
15051 3.845568e-26
15050 3.845568e-26
14800 5.945456e-26
20211 2.918915e-25
10201 1.874511e-24
10200 1.874511e-24
3630  2.020712e-23
3631  2.020712e-23
15240 4.477342e-23
4948  1.058164e-21
13317 1.368779e-20
20718 8.134032e-20
7543  1.469346e-19
21528 2.497172e-19
15239 1.043322e-18
20078 5.110969e-18
20077 5.110969e-18
20748 6.174915e-17
181   6.924383e-17
15063 9.526181e-17
15064 9.526181e-17
16811 8.763323e-16
4483  1.573807e-15
5180  2.884724e-15
13015 4.882499e-15
19376 4.882499e-15
13013 8.442157e-15
2420  2.797715e-14
2421  2.797715e-14
15672 1.377536e-13
15671 1.377536e-13
16563 2.654583e-13
8818  3.147295e-13
8819  3.147295e-13
7209  3.847790e-13
7208  3.847790e-13
4946  8.479721e-13
7852  1.144944e-11
7853  1.144944e-11
14822 1.422366e-11
15398 2.387561e-11
5048  2.948141e-11
9648  3.237754e-11
6702  3.318498e-11
23244 3.767872e-11
18915 5.483756e-11
18916 5.483756e-11
19378 1.178429e-10
15879 1.213319e-10
8391  2.507672e-10
12615 3.923652e-10
18619 4.004879e-10
6481  1.305394e-09
6480  1.305394e-09
3534  1.703501e-09
20745 1.718749e-09
5178  1.849278e-09
1118  2.352399e-09
15006 2.651967e-09
15007 2.651967e-09
21530 3.098336e-09
7088  3.491698e-09
7087  3.491698e-09
12301 3.499402e-09
1744  3.753644e-09
1745  3.753644e-09
17087 4.492818e-09
722   4.492818e-09
723   4.492818e-09
16181 5.072620e-09
16182 5.072620e-09
16562 5.788938e-09
4354  6.382609e-09
10498 6.382609e-09
10499 6.382609e-09
18805 6.574973e-09
18806 6.574973e-09
10623 6.754448e-09
10624 6.754448e-09
14091 8.963657e-09
14824 9.638510e-09
16862 1.025531e-08
1112  1.049317e-08
1111  1.049317e-08
22233 1.061817e-08
1480  1.201556e-08
1479  1.201556e-08
401   1.205514e-08
17131 1.677511e-08
13275 2.103824e-08
23401 2.489636e-08
21618 2.516249e-08
8743  2.715607e-08
16810 2.846341e-08
16015 2.846341e-08
6782  3.232253e-08
10415 3.666058e-08
5623  4.259372e-08
18038 4.350677e-08
18039 4.350677e-08
7745  4.494490e-08
7746  4.494490e-08
12051 5.242655e-08
16702 5.242655e-08
16703 5.242655e-08
8723  5.644398e-08
2037  5.744250e-08
7544  5.939982e-08
180   6.175234e-08
2899  6.491486e-08
2898  6.491486e-08
3293  7.904912e-08
22386 7.923710e-08
962   9.156028e-08
24977 1.170033e-07
15881 1.187444e-07
8394  1.254443e-07
18168 1.286850e-07
11592 1.439437e-07
6733  1.558159e-07
12170 1.558159e-07
12171 1.558159e-07
182   1.659139e-07
18398 1.710459e-07
22234 1.712289e-07
16858 1.712289e-07
16859 1.712289e-07
20209 2.671879e-07
20210 2.671879e-07
23243 3.622038e-07
17197 4.408653e-07
14329 4.467719e-07
14328 4.467719e-07
1718  4.467719e-07
1719  4.467719e-07
15716 5.026104e-07
19155 5.637010e-07
4252  5.771253e-07
4253  5.771253e-07
12052 5.771253e-07
17089 6.608598e-07
3923  6.837179e-07
22965 7.113876e-07
22966 7.113876e-07
15279 7.603156e-07
15280 7.603156e-07
17824 8.459178e-07
15276 8.621333e-07
15399 8.860081e-07
3533  9.146050e-07
13947 9.271961e-07
18873 9.691060e-07
22152 9.798490e-07
11479 1.123892e-06
11478 1.123892e-06
18617 1.231979e-06
15067 1.302313e-06
6854  1.330895e-06
6853  1.330895e-06
12577 1.424189e-06
16669 1.424189e-06
16670 1.424189e-06
19476 1.497034e-06
19477 1.497034e-06
8009  1.554455e-06
6734  1.793965e-06
166   1.841974e-06
14124 1.894787e-06
14361 1.898286e-06
11295 1.898286e-06
11296 1.898286e-06
6799  1.914937e-06
16852 1.914937e-06
16853 1.914937e-06
4087  1.995825e-06
12613 2.071319e-06
16062 2.095631e-06
17613 2.163320e-06
13872 2.201775e-06
4947  2.335101e-06
17553 2.436620e-06
25614 2.440395e-06
9455  2.502249e-06
8365  2.502249e-06
5512  2.509124e-06
24735 2.509124e-06
24734 2.509124e-06
2290  2.633623e-06
2291  2.633623e-06
24078 2.964765e-06
23875 3.172723e-06
23874 3.172723e-06
18090 3.277761e-06
6574  3.903536e-06
6573  3.903536e-06
23806 3.928238e-06
11420 4.669623e-06
9272  4.669623e-06
23448 4.704598e-06
23449 4.704598e-06
22798 4.910568e-06
13725 5.050706e-06
13726 5.050706e-06
26433 5.346344e-06
8487  5.500616e-06
12544 5.719457e-06
18400 5.817102e-06
731   5.830734e-06
732   5.830734e-06
6452  6.432369e-06
3295  7.391053e-06
2313  7.581465e-06
20979 7.743584e-06
7349  7.891530e-06
7350  7.891530e-06
18260 7.891530e-06
13590 8.273372e-06
4508  8.281126e-06
2219  9.611233e-06
24150 9.653131e-06
7279  1.022950e-05
18274 1.037180e-05
24978 1.079663e-05
24969 1.104940e-05
10625 1.199197e-05
7619  1.213356e-05
12332 1.224169e-05
14362 1.305741e-05
17119 1.380803e-05
8724  1.418142e-05
15261 1.439637e-05
21581 1.439637e-05
8032  1.585477e-05
2344  1.593451e-05
22764 1.620944e-05
13281 1.654701e-05
4607  1.654701e-05
8602  1.659171e-05
3140  1.664841e-05
25369 1.827595e-05
18452 2.044801e-05
5047  2.107556e-05
6783  2.258396e-05
8222  2.515458e-05
22742 2.515458e-05
3848  2.516351e-05
8271  2.538593e-05
8272  2.538593e-05
17563 2.538593e-05
12399 2.538593e-05
16392 2.740118e-05
3544  2.905866e-05
9125  2.949903e-05
5697  3.141418e-05
22461 3.164318e-05
399   3.174935e-05
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9611  1.615848e-02
25208 1.623025e-02
9413  1.624570e-02
9414  1.624570e-02
10331 1.637303e-02
10332 1.637303e-02
11104 1.640277e-02
26652 1.641495e-02
4401  1.641495e-02
4400  1.641495e-02
5435  1.645696e-02
17074 1.645986e-02
21626 1.645986e-02
21627 1.645986e-02
5625  1.645986e-02
2389  1.645986e-02
22287 1.650829e-02
19012 1.650989e-02
15161 1.651861e-02
7014  1.654412e-02
16337 1.654412e-02
13606 1.654412e-02
11373 1.662174e-02
11374 1.662174e-02
2711  1.685807e-02
15163 1.685807e-02
24770 1.686654e-02
15162 1.690754e-02
16185 1.704365e-02
1866  1.712615e-02
1868  1.712615e-02
25421 1.719539e-02
25420 1.719539e-02
23223 1.734719e-02
13436 1.749259e-02
12854 1.753921e-02
5455  1.766396e-02
224   1.777302e-02
26685 1.781726e-02
20421 1.801755e-02
20422 1.801755e-02
19019 1.811820e-02
19018 1.811820e-02
17721 1.811820e-02
12625 1.811820e-02
12624 1.811820e-02
18320 1.813549e-02
12546 1.819040e-02
7263  1.833731e-02
7262  1.833731e-02
23182 1.836125e-02
6828  1.841275e-02
7293  1.841275e-02
1508  1.841275e-02
5116  1.848446e-02
5115  1.848446e-02
3261  1.863859e-02
3355  1.868404e-02
3356  1.868404e-02
2197  1.868404e-02
16584 1.868404e-02
5552  1.868404e-02
5553  1.868404e-02
3827  1.872390e-02
1894  1.893773e-02
17733 1.904418e-02
22858 1.904418e-02
11864 1.905216e-02
5801  1.908435e-02
20682 1.909168e-02
4533  1.915167e-02
24769 1.917750e-02
23412 1.949213e-02
17377 1.954581e-02
8190  1.973290e-02
8191  1.973290e-02
8605  1.973687e-02
11004 1.973687e-02
11005 1.973687e-02
6823  1.973687e-02
17253 1.975329e-02
2109  1.981209e-02
7863  1.986658e-02
20929 2.023395e-02
10627 2.025948e-02
477   2.029200e-02
18994 2.031115e-02
3476  2.051364e-02
3477  2.051364e-02
21869 2.062122e-02
21870 2.062122e-02
6274  2.075782e-02
9879  2.081183e-02
13783 2.088902e-02
6114  2.090028e-02
21580 2.091167e-02
14209 2.106009e-02
22037 2.107826e-02
22038 2.107826e-02
23416 2.108897e-02
23417 2.108897e-02
26863 2.108897e-02
11424 2.109917e-02
22848 2.112123e-02
22849 2.112123e-02
2327  2.130193e-02
4039  2.138652e-02
22001 2.139672e-02
19851 2.148045e-02
5166  2.153558e-02
21183 2.160842e-02
17564 2.160842e-02
18217 2.177093e-02
10809 2.185101e-02
10235 2.206025e-02
20850 2.211740e-02
3094  2.217190e-02
4216  2.219253e-02
16055 2.219635e-02
25213 2.230447e-02
7588  2.232232e-02
15218 2.249957e-02
22980 2.250466e-02
22981 2.250466e-02
20851 2.263945e-02
11239 2.264231e-02
26705 2.273290e-02
26706 2.273290e-02
20687 2.295218e-02
3499  2.299161e-02
3500  2.299161e-02
20386 2.299161e-02
20387 2.299161e-02
10023 2.306024e-02
10489 2.306024e-02
13    2.333736e-02
9996  2.344953e-02
5698  2.350174e-02
22062 2.357302e-02
22061 2.357302e-02
6534  2.376521e-02
18273 2.376521e-02
12627 2.393868e-02
12872 2.405054e-02
12797 2.410085e-02
11268 2.434078e-02
5673  2.438122e-02
3070  2.440720e-02
169   2.445108e-02
16812 2.445108e-02
12044 2.445108e-02
895   2.452475e-02
1822  2.452475e-02
1823  2.452475e-02
15867 2.464370e-02
21021 2.477204e-02
21022 2.477204e-02
19015 2.477204e-02
19014 2.477204e-02
6619  2.477982e-02
18966 2.497940e-02
19078 2.511855e-02
19079 2.511855e-02
22942 2.511855e-02
20377 2.511855e-02
16364 2.511855e-02
10093 2.511855e-02
10094 2.511855e-02
4247  2.514630e-02
10285 2.521153e-02
10286 2.521153e-02
11240 2.538233e-02
6580  2.538233e-02
21333 2.547619e-02
11516 2.579671e-02
20937 2.594141e-02
2934  2.594141e-02
18469 2.643181e-02
2837  2.643181e-02
2836  2.643181e-02
10511 2.646502e-02
16357 2.657056e-02
16358 2.657056e-02
23346 2.667649e-02
23347 2.667649e-02
7587  2.670897e-02
11272 2.670897e-02
6642  2.670897e-02
6643  2.670897e-02
8184  2.683183e-02
4381  2.688522e-02
6855  2.688522e-02
6856  2.688522e-02
3902  2.693918e-02
9174  2.695721e-02
5176  2.711039e-02
21446 2.711039e-02
10468 2.731967e-02
10827 2.733515e-02
14123 2.747219e-02
23701 2.752090e-02
3315  2.757119e-02
16929 2.757119e-02
10183 2.757119e-02
17722 2.758039e-02
14217 2.809614e-02
16217 2.819174e-02
9244  2.823078e-02
9245  2.823078e-02
19659 2.838381e-02
24154 2.860190e-02
19511 2.864771e-02
12585 2.865807e-02
12586 2.865807e-02
5054  2.869599e-02
4331  2.874695e-02
14207 2.875139e-02
12131 2.875139e-02
2520  2.875139e-02
16001 2.882590e-02
21894 2.882590e-02
24125 2.886956e-02
26333 2.891768e-02
18091 2.891768e-02
3115  2.894276e-02
17414 2.918770e-02
17415 2.918770e-02
15768 2.938487e-02
7884  2.938487e-02
12961 2.938487e-02
12962 2.938487e-02
22917 2.940976e-02
22392 2.942741e-02
12061 2.954876e-02
9422  2.954876e-02
9423  2.954876e-02
16971 2.954876e-02
4845  2.954876e-02
22729 2.968200e-02
22730 2.968200e-02
25977 2.968200e-02
18754 2.968200e-02
18755 2.968200e-02
20379 2.975248e-02
26774 3.012316e-02
23273 3.026702e-02
23274 3.026702e-02
17168 3.030366e-02
18708 3.031468e-02
13294 3.064942e-02
24800 3.092056e-02
19069 3.094167e-02
12241 3.103625e-02
12242 3.103625e-02
7756  3.113682e-02
5040  3.113682e-02
1020  3.113682e-02
19832 3.113682e-02
19833 3.113682e-02
7942  3.122973e-02
7943  3.122973e-02
13240 3.130221e-02
13239 3.130221e-02
12853 3.139946e-02
20922 3.168315e-02
16312 3.169848e-02
16313 3.169848e-02
6882  3.169848e-02
13788 3.171260e-02
17813 3.171260e-02
11061 3.185830e-02
15722 3.185830e-02
15721 3.185830e-02
8506  3.185830e-02
6072  3.197895e-02
6073  3.197895e-02
11865 3.200012e-02
8407  3.202131e-02
8408  3.202131e-02
12822 3.202131e-02
12823 3.202131e-02
16797 3.206978e-02
15715 3.206978e-02
18876 3.206978e-02
3898  3.216505e-02
21001 3.216505e-02
15181 3.236170e-02
14839 3.239615e-02
376   3.239615e-02
377   3.239615e-02
7586  3.239615e-02
15471 3.252197e-02
19836 3.276983e-02
19837 3.276983e-02
15144 3.285613e-02
15145 3.285613e-02
21858 3.291971e-02
2039  3.305317e-02
17255 3.334039e-02
4986  3.352613e-02
17735 3.355493e-02
26653 3.358768e-02
24712 3.358768e-02
24430 3.358768e-02
24429 3.358768e-02
23194 3.358768e-02
2253  3.371067e-02
4174  3.408626e-02
1649  3.428371e-02
9883  3.434237e-02
11522 3.434237e-02
16768 3.434237e-02
8576  3.434559e-02
13502 3.446509e-02
8373  3.448057e-02
14139 3.448057e-02
20683 3.452093e-02
19013 3.488029e-02
2200  3.507071e-02
14476 3.513307e-02
14475 3.513307e-02
14593 3.513307e-02
14594 3.513307e-02
11515 3.519650e-02
1671  3.558017e-02
4672  3.558233e-02
6800  3.572184e-02
13293 3.598884e-02
17718 3.622572e-02
17719 3.622572e-02
18998 3.622572e-02
10244 3.622572e-02
12905 3.630525e-02
19037 3.630525e-02
17854 3.630525e-02
13263 3.636805e-02
8480  3.637308e-02
1534  3.637308e-02
3507  3.640230e-02
45    3.663517e-02
21735 3.669262e-02
7337  3.689780e-02
7338  3.689780e-02
6824  3.689780e-02
7785  3.689780e-02
7784  3.689780e-02
16723 3.689780e-02
20902 3.692652e-02
6449  3.692652e-02
15573 3.692652e-02
4128  3.702678e-02
2091  3.706132e-02
2092  3.706132e-02
22018 3.714764e-02
22017 3.714764e-02
12628 3.720567e-02
26393 3.720567e-02
26392 3.720567e-02
9952  3.720567e-02
1008  3.742114e-02
1007  3.742114e-02
17812 3.754815e-02
9129  3.761682e-02
12302 3.777472e-02
12303 3.777472e-02
15282 3.781852e-02
6683  3.783903e-02
19301 3.783903e-02
19302 3.783903e-02
19765 3.786405e-02
14981 3.786714e-02
15342 3.842760e-02
21959 3.849082e-02
3416  3.863267e-02
3417  3.863267e-02
20435 3.932284e-02
20436 3.932284e-02
5442  3.951010e-02
5441  3.951010e-02
16528 3.960910e-02
16529 3.960910e-02
8150  3.963343e-02
8151  3.963343e-02
15447 3.969500e-02
23323 3.969500e-02
23322 3.969500e-02
4443  3.969500e-02
4442  3.969500e-02
3709  3.971251e-02
25409 3.981438e-02
8195  3.987956e-02
15599 3.995114e-02
12753 4.009779e-02
8745  4.009779e-02
15156 4.017043e-02
17248 4.017043e-02
6978  4.054749e-02
17740 4.058579e-02
10028 4.058579e-02
5     4.058579e-02
13448 4.060188e-02
9609  4.060188e-02
1959  4.065212e-02
1960  4.065212e-02
25516 4.072476e-02
11669 4.072476e-02
11670 4.072476e-02
663   4.096675e-02
7235  4.099768e-02
16950 4.139909e-02
11063 4.141317e-02
14157 4.147985e-02
11901 4.147985e-02
5168  4.148183e-02
22972 4.176030e-02
15618 4.180694e-02
24701 4.220202e-02
21796 4.225930e-02
13011 4.226738e-02
13012 4.226738e-02
17674 4.229519e-02
12550 4.230281e-02
13472 4.239326e-02
18150 4.250222e-02
21399 4.263858e-02
3250  4.267353e-02
4135  4.290729e-02
18344 4.292397e-02
2654  4.292397e-02
22609 4.292880e-02
22608 4.292880e-02
5050  4.309141e-02
17132 4.361699e-02
23216 4.366078e-02
4468  4.368542e-02
16706 4.373002e-02
14778 4.373002e-02
14779 4.373002e-02
6151  4.377854e-02
3262  4.378308e-02
952   4.382244e-02
953   4.382244e-02
16803 4.383132e-02
16804 4.383132e-02
21492 4.383132e-02
21493 4.383132e-02
11917 4.383132e-02
18663 4.387619e-02
18664 4.387619e-02
23562 4.389660e-02
3566  4.429404e-02
25615 4.441122e-02
15819 4.458480e-02
24906 4.458480e-02
18008 4.458480e-02
17474 4.458480e-02
3897  4.461380e-02
10233 4.484959e-02
10234 4.484959e-02
9684  4.499997e-02
18733 4.506677e-02
18734 4.506677e-02
22860 4.506677e-02
9202  4.506677e-02
5935  4.506677e-02
7892  4.522186e-02
7893  4.522186e-02
353   4.539084e-02
354   4.539084e-02
18185 4.551363e-02
18186 4.551363e-02
20855 4.551363e-02
20856 4.551363e-02
13605 4.555682e-02
11190 4.570320e-02
13933 4.590087e-02
17662 4.612992e-02
3098  4.615009e-02
17055 4.617592e-02
9941  4.617592e-02
16974 4.625481e-02
9700  4.627455e-02
6451  4.628245e-02
2222  4.630666e-02
1099  4.666966e-02
5714  4.706445e-02
5713  4.706445e-02
17572 4.715555e-02
17573 4.715555e-02
4894  4.751282e-02
21317 4.769955e-02
23335 4.769955e-02
20225 4.800729e-02
20226 4.800729e-02
15574 4.800729e-02
3574  4.800729e-02
3178  4.802983e-02
17177 4.809818e-02
14141 4.812388e-02
23508 4.825895e-02
18318 4.862397e-02
18319 4.862397e-02
23563 4.866387e-02
5192  4.866387e-02
5193  4.866387e-02
2394  4.900163e-02
23164 4.900163e-02
11521 4.904808e-02
19815 4.904808e-02
19156 4.933602e-02
24931 4.941613e-02
9246  4.941613e-02
6598  4.959743e-02

length(idx.txp)

[1] 1459

pvalue may contain NA values which may cause downstream errors (in stagewise analysis by stageR) so they are converted to 1`s.

no.na <- function(x) ifelse(is.na(x), 1, x)
res$pvalue <- no.na(res$pvalue)
res.txp$pvalue <- no.na(res.txp$pvalue)

Plotting

For a given gene, plot the observed and estimated with Dirichlet-multinomial model feature proportions in each group. Estimated group proportions are marked with diamond shapes.

top_gene_id <- res$gene_id[1]
plotProportions(d, gene_id = top_gene_id, group_variable = "day")

plotProportions(d, gene_id = top_gene_id, group_variable = "day", 
  plot_type = "lineplot")

Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
of ggplot2 3.3.4.
ℹ The deprecated feature was likely used in the DRIMSeq package.
  Please report the issue to the authors.

plotProportions(d, gene_id = top_gene_id, group_variable = "day", 
  plot_type = "ribbonplot")

Coordinate system already present. Adding new coordinate system, which will
replace the existing one.

StageR following DRIMSeq

stageR package does stage-wise analysis of data, by screening first at the gene level for evidence of DTU (screening stage) and confirms which trancsripts within those significant genes show evidence of DTU (confirmation stage).

nrow(res)

[1] 9901

A vector of per-gene p-values pScreen for the screening stage is constructed. Addiionally, the gene and transcript version numbers are stripped from their Ensembl IDs (only first 15 characters are kept).

pScreen <- res$pvalue
strp <- function(x) substr(x,1,15)
names(pScreen) <- strp(res$gene_id)

A one column matrix of the confirmation p-values pConfirmation is constructed:

pConfirmation <- matrix(res.txp$pvalue, ncol=1)
rownames(pConfirmation) <- strp(res.txp$feature_id)

A two column dataframe tx2genewith the transcript and gene identifiers is arranged:

tx2gene <- res.txp[,c("feature_id", "gene_id")]
for (i in 1:2) tx2gene[,i] <- strp(tx2gene[,i])

stageR analysis is perform with overall false discovery rate (OFDR, alpha parameter) equal to 0.05.

stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation,
                      pScreenAdjusted=FALSE, tx2gene=tx2gene)
stageRObj <- stageWiseAdjustment(stageRObj, method="dtu", alpha=0.05)
suppressWarnings({
  drim.padj <- getAdjustedPValues(stageRObj, order=FALSE,
                                  onlySignificantGenes=TRUE)
})

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

head(drim.padj)

           geneID            txID         gene   transcript
1 ENSG00000112759 ENST00000371755 8.889936e-61 0.000000e+00
2 ENSG00000112759 ENST00000393844 8.889936e-61 0.000000e+00
3 ENSG00000107554 ENST00000543621 1.221282e-36 5.097696e-40
4 ENSG00000172889 ENST00000371698 6.446990e-33 0.000000e+00
5 ENSG00000172889 ENST00000406555 6.446990e-33 0.000000e+00
6 ENSG00000164587 ENST00000312037 1.866405e-31 4.249832e-34

nrow(drim.padj)

[1] 3149

The data.frame dex.padj summarizes the adjusted p-values from the two-stage analysis. Only genes that passed the filter (screening) are included in the table. The transcripts (column trancsript) with values less than 0.05 (5 % OFDR) pass the confirmation stage.

DEXSeq

The filtered DRIMSeq object is used for DEXSeq workflow, as the filtering is easier, and the analysis is sped up. DEXSeqDataSet is built from d, filtered DRIMseq object, sample information (sample.data), a design formula, transcript ID and gene ID:

sample.data <- DRIMSeq::samples(d)
# We start with already filtered DRIMSeq object
count.data <- round(as.matrix(counts(d)[,-c(1:2)]))
dxd <- DEXSeqDataSet(countData=count.data,
                     sampleData=sample.data,
                     design=~sample + exon + day:exon,
                     featureID=counts(d)$feature_id,
                     groupID=counts(d)$gene_id)

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

DEXSeq analysis is performed using the following 3 functions: (1) estimation of size factors using estimateSizeFactors, (2) estimation of dispersion estimateDispersions, then (3) perform a likelihood ratio test for differential exon usage (in this case, transcripts) testForDEU.

system.time({
  dxd <- estimateSizeFactors(dxd)
  dxd <- estimateDispersions(dxd, quiet=TRUE)
  dxd <- testForDEU(dxd, reducedModel=~sample + exon)
})

24 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

   user  system elapsed 
129.169   0.180 129.493 

The results tables (log2 fold changes and p-values) can be generated using the DEXSeqResultsfunction and perGeneQValue function is used to compute a per-gene adjusted p-value.

dxr <- DEXSeqResults(dxd, independentFiltering=FALSE)
qval <- perGeneQValue(dxr)
# Per gene
dxr.g <- data.frame(gene=names(qval),qval)
# Per transcript
dxr.t = as.data.frame(dxr[, c("featureID","groupID","pvalue")])
head(dxr.g)

                                 gene         qval
ENSG00000000005.6   ENSG00000000005.6 1.000000e+00
ENSG00000000457.14 ENSG00000000457.14 9.537975e-01
ENSG00000000460.17 ENSG00000000460.17 9.362627e-08
ENSG00000001084.13 ENSG00000001084.13 3.136415e-01
ENSG00000001167.15 ENSG00000001167.15 1.000000e+00
ENSG00000001460.18 ENSG00000001460.18 1.198466e-01

Results:

# Number of identified genes showing evidence for DTU
nrow(dxr.g[dxr.g$qval < 0.05,])

[1] 1457

# Number of transcripts involved
nrow(dxr[dxr$padj < 0.05,])

[1] 2409

stageR following DEXSeq

The code for the procedure is similar to DRIMSeq procedure, with alpha=0.05.

strp <- function(x) substr(x,1,15)
pConfirmation <- matrix(dxr$pvalue,ncol=1)
dimnames(pConfirmation) <- list(strp(dxr$featureID),"transcript")
pScreen <- qval
names(pScreen) <- strp(names(pScreen))
tx2gene <-  data.frame(dxr.t[,c("featureID", "groupID")], 
dxr.t[,c("featureID", "groupID")])
for (i in 1:2) tx2gene[,i] = strp(tx2gene[,i])
stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation,
                      pScreenAdjusted=TRUE, tx2gene=tx2gene[1:2])
stageRObj = stageRTx(pScreen = pScreen, 
pConfirmation = pConfirmation, 
pScreenAdjusted = TRUE, 
tx2gene = tx2gene[1:2])

stageRObj = stageWiseAdjustment(stageRObj, method = "dtu", alpha = 0.05)

suppressWarnings({
  dex.padj <- getAdjustedPValues(stageRObj, order=FALSE,
                                 onlySignificantGenes=TRUE)
})

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

dex.padj = merge(tx2gene, dex.padj, by.x = c("groupID","featureID"), by.y = c("geneID","txID"))

head(dex.padj)

          groupID       featureID       featureID.1          groupID.1
1 ENSG00000000460       BambuTx12         BambuTx12 ENSG00000000460.17
2 ENSG00000000460 ENST00000359326 ENST00000359326.9 ENSG00000000460.17
3 ENSG00000001497 ENST00000374807 ENST00000374807.9 ENSG00000001497.18
4 ENSG00000001497 ENST00000374811 ENST00000374811.8 ENSG00000001497.18
5 ENSG00000001497 ENST00000677834 ENST00000677834.1 ENSG00000001497.18
6 ENSG00000001497 ENST00000678602 ENST00000678602.1 ENSG00000001497.18
          gene   transcript
1 9.362627e-08 0.000000e+00
2 9.362627e-08 0.000000e+00
3 2.793368e-11 2.037362e-04
4 2.793368e-11 2.467069e-12
5 2.793368e-11 2.037362e-04
6 2.793368e-11 1.000000e+00

length(unique(dex.padj[dex.padj$gene < 0.05,]$groupID))

[1] 1457

table(dex.padj$transcript < 0.05)

FALSE  TRUE 
 2315  2358 

Exporting the results

dex.norm = cbind(as.data.frame(stringr::str_split_fixed(rownames(counts(dxd)), ":", 2)), as.data.frame(counts(dxd, normalized = TRUE))[,1:20])
colnames(dex.norm) = c("groupID", "featureID", as.character(colData(dxd)$sample_id)[1:20])
row.names(dex.norm) = NULL
# Per-group normalised mean
dex.mean = as.data.frame(sapply( levels(samps$day), 
function(lvl) rowMeans(dex.norm[, 3:ncol(dex.norm)][, samps$day == lvl, drop = FALSE]) ))
colnames(dex.mean) <- paste0("mean.day", colnames(dex.mean))

# log2 fold change in expression
dex.log2fc = log2(dex.mean[2]/dex.mean[1])
colnames(dex.log2fc) = "log2fc"
rownames(dex.log2fc) = dex.norm$featureID

# Merge to create result data
dexData = cbind(dex.norm[,1:2], dex.mean, dex.norm[, 3:ncol(dex.norm)])
colnames(dexData)[1:2] <-  c("GeneID","TranscriptID")
dexData = dexData[order(dexData$GeneID, dexData$TranscriptID),]

# Merge to create result data
dexDTU = merge(dex.padj[,c("featureID.1","groupID.1","gene","transcript")], dex.log2fc, by.x = "featureID.1", by.y = "row.names")
colnames(dexDTU)[1:2] <-  c("TranscriptID","GeneID")
dexDTU = dexDTU[order(dexDTU$GeneID, dexDTU$TranscriptID),]

# Write results to files
write.table(dexData, file="DTU_DEXSeq-stageR_means_and_counts.txt", sep = "\t", quote = F, row.names = F, col.names = T)
write.table(dexDTU, file="DTU_DEXSeq-stageR_results.txt", sep = "\t", quote = F, row.names = F, col.names = T)

Plotting

A custom function plotExpression was made to plot the transcript expression of a given gene as from .

# We will use this function in both DRIMSeq & DEXSeq workflows
plotExpression <- function(expData = NULL, geneID = NULL, samps = NULL, isProportion = FALSE) {
        colnames(expData)[1:2] = c("gid","tid")
        sub = subset(expData, gid == geneID)
        print(sub)
        sub = reshape2::melt(sub, id = c("gid", "tid"))
        sub = merge(samps, sub, by.x = "sample_id", by.y = "variable")
        print(sub)
        if(!isProportion) {
                sub$value = log(sub$value)
        }
        print(sub)

        clrs = c("dodgerblue3", "maroon2",  "forestgreen", "darkorange1", "blueviolet", "firebrick2",
"deepskyblue", "orchid2", "chartreuse3", "gold", "slateblue1", "tomato" , "blue", "magenta", "green3",
"yellow", "purple3", "red" ,"darkslategray1", "lightpink1", "lightgreen", "khaki1", "plum3", "salmon")

        p = ggplot(sub, aes(tid, value, color = day, fill = day)) +
        geom_boxplot(alpha = 0.4, outlier.shape = NA, width = 0.8, lwd = 0.5) +
        stat_summary(fun = mean, geom = "point", color = "black", shape = 5, size = 3, position=position_dodge(width = 0.8)) +
        scale_color_manual(values = clrs) + scale_fill_manual(values = clrs) +
        geom_quasirandom(color = "black", size = 1, dodge.width = 0.8) + theme_bw() +
        ggtitle(geneID) + xlab("Transcripts")

        if(!isProportion) {
                p = p + ylab("log(Expression)")
        } else {
                p = p + ylab("Proportions")
        }
        p
}

# Plot the normalised counts for one of the significant genes, where we can see evidence of switching
gene_id <-  unique(dex.padj[order(dex.padj$transcript, dex.padj$gene),]$groupID.1)[1]
plotExpression(dex.norm, gene_id, samps, isProportion = T)

                     gid               tid day0.rep1 day0.rep2 day0.rep3
10848 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
10849 ENSG00000010671.17 ENST00000621635.4  34.31592  18.37981  21.88111
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
10848  3.851982  62.56142  915.4916 849.848827 2210.95863 2283.79343 1188.60736
10849 33.704846   0.00000    0.0000   8.484348   57.94087   28.49262   46.59708
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
10848 1114.01421    34.31592    18.37981    21.88111   33.704846     0.00000
10849   41.62983     0.00000     0.00000     0.00000    3.851982    62.56142
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
10848      0.0000    8.484348    57.94087    28.49262
10849    915.4916  849.848827  2210.95863  2283.79343
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.315922
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.379814
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.881106
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.851982
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.704846
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.561421
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.491563
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.848827
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.484348
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.940870
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.492624
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.597075
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.629829
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.315922
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.379814
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.881106
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.851982
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.704846
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.561421
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.491563
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.848827
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.484348
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.940870
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.492624
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.597075
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.629829

Comparison of DRIMSeq and DEXSeq

Number of identified transcripts from DEXSeq:

dim(dex.padj[order(dex.padj$gene, decreasing = T), ])

[1] 4673    6

Number of identified transcripts from DRIMSeq:

dim(drim.padj[order(drim.padj$gene, decreasing = T), ])

[1] 3149    4

Check the intersection between the different methods for screened genes:

length(intersect(dex.padj$groupID, drim.padj$geneID))

[1] 553

venn <- list(DEX = dex.padj$groupID, DRIM = drim.padj$geneID)
ggvenn(venn)

Check the intersection between the different methods for features:

length(intersect(dex.padj$featureID, drim.padj$txID))

[1] 1796

venn <- list(DEX = dex.padj$featureID, DRIM = drim.padj$txID)
ggvenn(venn)

Making a function for the pipeline using DEXSeq x DRIMSeq

samps <- df_list_meta$metadata
samps <- samps %>% column_to_rownames(var="sampleID")
colnames(samps) <- c("sample_id", "day")
samps$day <- factor(samps$day)

DTU <- function(salmon, txdf, sample_name, n = 11, n.small = 11){
  # DRIMSeq Filtering
  cts <- salmon
  colnames(cts) <- samps$sample_id
  counts <- data.frame(gene_id=txdf$gene_id,
                     feature_id=rownames(txdf),
                     cts)
  d <- dmDSdata(counts=counts, samples=samps)
  d <- dmFilter(d,
                min_samps_feature_expr=n.small, min_feature_expr=10,
                min_samps_feature_prop=n.small, min_feature_prop=0.1,
                min_samps_gene_expr=n, min_gene_expr=10)
  print(plotData(d))
  png(paste0(sample_name, "plotData.DEXSeq-stageR.png"), width=6, height=6, units = "in", res = 300)
  print(plotData(d))
  dev.off()
  print(table(table(counts(d)$gene_id)))
  sample.data <- DRIMSeq::samples(d)
  
  # DEXSeq
  count.data <- round(as.matrix(counts(d)[,-c(1:2)]))
  dxd <- DEXSeqDataSet(countData=count.data,
                       sampleData=sample.data,
                       design=~sample + exon + day:exon,
                       featureID=counts(d)$feature_id,
                       groupID=counts(d)$gene_id)
  dxd <- estimateSizeFactors(dxd)
  dxd <- estimateDispersions(dxd, quiet=TRUE)
  dxd <- testForDEU(dxd, reducedModel=~sample + exon)
  dxr <- DEXSeqResults(dxd, independentFiltering=FALSE)
  qval <- perGeneQValue(dxr)
  # Per gene
  dxr.g <- data.frame(gene=names(qval),qval)
  # Per transcript
  dxr.t = as.data.frame(dxr[, c("featureID","groupID","pvalue")])
  # Number of identified genes showing evidence for DTU
  print(nrow(dxr.g[dxr.g$qval < 0.05,]))
  # Number of transcripts involved
  print(nrow(dxr[dxr$padj < 0.05,]))

  # stageR
  strp <- function(x) substr(x,1,15)
  pConfirmation <- matrix(dxr$pvalue,ncol=1)
  dimnames(pConfirmation) <- list(strp(dxr$featureID),"transcript")
  pScreen <- qval
  names(pScreen) <- strp(names(pScreen))
  tx2gene <-  data.frame(dxr.t[,c("featureID", "groupID")], 
  dxr.t[,c("featureID", "groupID")])
  for (i in 1:2) tx2gene[,i] = strp(tx2gene[,i])
  stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation,
                        pScreenAdjusted=TRUE, tx2gene=tx2gene[1:2])
  stageRObj = stageRTx(pScreen = pScreen, 
  pConfirmation = pConfirmation, 
  pScreenAdjusted = TRUE, 
  tx2gene = tx2gene[1:2])
  
  stageRObj = stageWiseAdjustment(stageRObj, method = "dtu", alpha = 0.05)
  
  suppressWarnings({
    dex.padj <- getAdjustedPValues(stageRObj, order=FALSE,
                                   onlySignificantGenes=TRUE)
  })
  
  dex.padj = merge(tx2gene, dex.padj, by.x = c("groupID","featureID"), by.y = c("geneID","txID"))
  print(head(dex.padj[order(dex.padj$gene, decreasing = T), ]))
  
  # Normalize counts
  dex.norm = cbind(as.data.frame(stringr::str_split_fixed(rownames(counts(dxd)), ":", 2)), as.data.frame(counts(dxd, normalized = TRUE))[,1:20])
  colnames(dex.norm) = c("groupID", "featureID", as.character(colData(dxd)$sample_id)[1:20])
  row.names(dex.norm) = NULL

  # Per-group normalised mean
  dex.mean = as.data.frame(sapply( levels(samps$day), 
  function(lvl) rowMeans(dex.norm[, 3:ncol(dex.norm)][, samps$day == lvl, drop = FALSE]) ))
  colnames(dex.mean) <- paste0("mean.day", colnames(dex.mean))
  
  # log2 fold change in expression
  dex.log2fc = log2(dex.mean[2]/dex.mean[1])
  colnames(dex.log2fc) = "log2fc"
  rownames(dex.log2fc) = dex.norm$featureID
  
  # Merge to create result data
  dexData = cbind(dex.norm[,1:2], dex.mean, dex.norm[, 3:ncol(dex.norm)])
  colnames(dexData)[1:2] <-  c("GeneID","TranscriptID")
  dexData = dexData[order(dexData$GeneID, dexData$TranscriptID),]
  
  # Merge to create result data
  dexDTU = merge(dex.padj[,c("featureID.1","groupID.1","gene","transcript")], dex.log2fc, by.x = "featureID.1", by.y = "row.names")
  colnames(dexDTU)[1:2] <-  c("TranscriptID","GeneID")
  dexDTU = dexDTU[order(dexDTU$GeneID, dexDTU$TranscriptID),]
  
  # Write results to files
  write.table(dexData, file=paste0(sample_name, "DTU_DEXSeq-stageR_means_and_counts.txt"), sep = "\t", quote = F, row.names = F, col.names = T)
  write.table(dexDTU, file=paste0(sample_name, "DTU_DEXSeq-stageR_results.txt"), sep = "\t", quote = F, row.names = F, col.names = T)

  # Plot the normalised counts for one of the significant genes, where we can see evidence of switching
  gene_id <-  unique(dex.padj[order(dex.padj$transcript, dex.padj$gene),]$groupID.1)[1]
  
  print(plotExpression(dex.norm, gene_id, samps, isProportion = T))
  png(paste0(sample_name, "plotExpression-stageR.png"), width=6, height=6, units = "in", res = 300)
  print(plotExpression(dex.norm, gene_id, samps, isProportion = T))
  dev.off()
  
  return(dexDTU)
}

NDR 0.025

# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.025
res_salmon_0.025 <- DTU(salmon_0.025, txdf, "salmon_0.025.", n = 3, n.small = 3)

   2    3    4    5    6    7    8    9 
5214 2887 1213  433  114   29    8    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

24 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 1457
[1] 2409

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID       featureID.1          groupID.1
3614 ENSG00000179603 ENST00000339582 ENST00000339582.7 ENSG00000179603.18
3615 ENSG00000179603 ENST00000358373 ENST00000358373.7 ENSG00000179603.18
3616 ENSG00000179603 ENST00000457830 ENST00000457830.1 ENSG00000179603.18
3617 ENSG00000179603 ENST00000472701 ENST00000472701.5 ENSG00000179603.18
2982 ENSG00000164162 ENST00000309439 ENST00000309439.9 ENSG00000164162.14
2983 ENSG00000164162 ENST00000451299 ENST00000451299.6 ENSG00000164162.14
           gene transcript
3614 0.04999221 0.63208638
3615 0.04999221 0.03665347
3616 0.04999221 1.00000000
3617 0.04999221 0.04462491
2982 0.04992877 1.00000000
2983 0.04992877 0.03658163
                     gid               tid day0.rep1 day0.rep2 day0.rep3
10848 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
10849 ENSG00000010671.17 ENST00000621635.4  34.31592  18.37981  21.88111
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
10848  3.851982  62.56142  915.4916 849.848827 2210.95863 2283.79343 1188.60736
10849 33.704846   0.00000    0.0000   8.484348   57.94087   28.49262   46.59708
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
10848 1114.01421    34.31592    18.37981    21.88111   33.704846     0.00000
10849   41.62983     0.00000     0.00000     0.00000    3.851982    62.56142
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
10848      0.0000    8.484348    57.94087    28.49262
10849    915.4916  849.848827  2210.95863  2283.79343
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.315922
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.379814
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.881106
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.851982
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.704846
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.561421
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.491563
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.848827
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.484348
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.940870
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.492624
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.597075
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.629829
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.315922
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.379814
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.881106
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.851982
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.704846
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.561421
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.491563
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.848827
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.484348
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.940870
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.492624
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.597075
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.629829

                     gid               tid day0.rep1 day0.rep2 day0.rep3
10848 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
10849 ENSG00000010671.17 ENST00000621635.4  34.31592  18.37981  21.88111
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
10848  3.851982  62.56142  915.4916 849.848827 2210.95863 2283.79343 1188.60736
10849 33.704846   0.00000    0.0000   8.484348   57.94087   28.49262   46.59708
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
10848 1114.01421    34.31592    18.37981    21.88111   33.704846     0.00000
10849   41.62983     0.00000     0.00000     0.00000    3.851982    62.56142
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
10848      0.0000    8.484348    57.94087    28.49262
10849    915.4916  849.848827  2210.95863  2283.79343
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.315922
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.379814
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.881106
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.851982
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.704846
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.561421
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.491563
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.848827
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.484348
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.940870
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.492624
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.597075
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.629829
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.315922
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.379814
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.881106
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.851982
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.704846
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.561421
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.491563
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.848827
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.484348
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.940870
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.492624
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.597075
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.629829

res_bambu_0.025 <- DTU(bambu_0.025, txdf,  "bambu_0.025.", n = 3, n.small = 3)

   2    3    4    5    6    7    8 
4598 1698  583  157   40    9    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

12 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 3166
[1] 6967

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID        featureID.1          groupID.1
8315 ENSG00000253352 ENST00000519077  ENST00000519077.4 ENSG00000253352.10
8316 ENSG00000253352 ENST00000644027  ENST00000644027.1 ENSG00000253352.10
8317 ENSG00000253352 ENST00000644773  ENST00000644773.2 ENSG00000253352.10
6150 ENSG00000173928 ENST00000312423  ENST00000312423.4  ENSG00000173928.4
6151 ENSG00000173928 ENST00000674460  ENST00000674460.1  ENSG00000173928.4
3467 ENSG00000135316 ENST00000355238 ENST00000355238.11 ENSG00000135316.19
           gene transcript
8315 0.04979806 0.02006134
8316 0.04979806 0.65219686
8317 0.04979806 1.00000000
6150 0.04972598 0.00000000
6151 0.04972598 0.00000000
3467 0.04966156 1.00000000
                    gid                tid day0.rep1 day0.rep2 day0.rep3
3562 ENSG00000004864.14 ENST00000265631.10  2368.620  1969.083  2190.773
3563 ENSG00000004864.14  ENST00000416240.6  2978.493  2123.488  2322.238
     day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
3562  2263.717  3309.664  2385.386  2362.016  1885.506     0.000     0.000
3563  2462.271  3309.664  2580.530  2362.016  1885.506  3183.399  3399.719
     day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
3562     0.000    2978.493    2123.488    2322.238    2462.271    3309.664
3563  2976.813    2368.620    1969.083    2190.773    2263.717    3309.664
     day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
3562    2580.530    2362.016    1885.506    3183.399
3563    2385.386    2362.016    1885.506       0.000
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2978.493
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2368.620
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1969.083
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.488
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2190.773
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2322.238
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2263.717
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2462.271
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3309.664
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2580.530
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2362.016
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1885.506
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3183.399
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3399.719
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2976.813
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2978.493
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2368.620
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1969.083
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.488
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2190.773
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2322.238
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2263.717
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2462.271
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3309.664
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2580.530
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2362.016
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1885.506
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3183.399
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3399.719
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2976.813

                    gid                tid day0.rep1 day0.rep2 day0.rep3
3562 ENSG00000004864.14 ENST00000265631.10  2368.620  1969.083  2190.773
3563 ENSG00000004864.14  ENST00000416240.6  2978.493  2123.488  2322.238
     day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
3562  2263.717  3309.664  2385.386  2362.016  1885.506     0.000     0.000
3563  2462.271  3309.664  2580.530  2362.016  1885.506  3183.399  3399.719
     day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
3562     0.000    2978.493    2123.488    2322.238    2462.271    3309.664
3563  2976.813    2368.620    1969.083    2190.773    2263.717    3309.664
     day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
3562    2580.530    2362.016    1885.506    3183.399
3563    2385.386    2362.016    1885.506       0.000
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2978.493
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2368.620
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1969.083
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.488
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2190.773
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2322.238
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2263.717
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2462.271
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3309.664
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2580.530
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2362.016
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1885.506
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3183.399
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3399.719
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2976.813
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2978.493
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2368.620
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1969.083
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.488
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2190.773
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2322.238
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2263.717
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2462.271
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3309.664
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2580.530
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2362.016
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1885.506
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3183.399
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3399.719
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2976.813

confirmed_salmon_0.025 <- res_salmon_0.025[res_salmon_0.025$transcript < 0.05, ]
nrow(confirmed_salmon_0.025)

[1] 2358

confirmed_bambu_0.025 <- res_bambu_0.025[res_bambu_0.025$transcript < 0.05, ]
nrow(confirmed_bambu_0.025)

[1] 6316

For Illumina+Salmon, out of the 9901 tested genes and 27084 tested features, DEXSeq test identified 1457 genes showing evidence of isoform switching involving 2409 transcripts. For PacBio+Bambu out of the 7088 tested genes and 17734 tested features, 3166 genes involving 6967 trancsripts were identified.

After the stageR procedure, 2358 transcripts passed the confirmation stage for Illumina+Salmon and 6316 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.

Upset Plot

# Screened Genes
length(intersect(confirmed_salmon_0.025$GeneID, confirmed_bambu_0.025$GeneID))

[1] 742

venn <- list(SALMON = confirmed_salmon_0.025$GeneID, BAMBU = confirmed_bambu_0.025$GeneID)
ggvenn(venn)

upset(fromList(venn))

# Confirmed Transcripts
length(intersect(confirmed_salmon_0.025$TranscriptID, confirmed_bambu_0.025$TranscriptID))

[1] 834

venn <- list(SALMON = confirmed_salmon_0.025$TranscriptID, BAMBU = confirmed_bambu_0.025$TranscriptID)
ggvenn(venn)

upset(fromList(venn))

From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 11 %.

Comparsion of pAdj and logFC

both_detected <-
  intersect(res_bambu_0.025$TranscriptID, res_salmon_0.025$TranscriptID)
sorted_res_salmon_0.025 <- res_salmon_0.025[order(res_salmon_0.025$TranscriptID),]
both_sorted_res_salmon_0.025 <- sorted_res_salmon_0.025[which(sorted_res_salmon_0.025$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.025 <- res_bambu_0.025[order(res_bambu_0.025$TranscriptID),]
both_sorted_res_bambu_0.025 <- sorted_res_bambu_0.025[which(sorted_res_bambu_0.025$TranscriptID %in% both_detected), ]

padj <- data.frame(Salmon = both_sorted_res_salmon_0.025$transcript, Bambu = both_sorted_res_bambu_0.025$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of P-values (NDR=0.025)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

Warning: Removed 663 rows containing non-finite values (`stat_smooth()`).

logfc <- data.frame(Salmon = both_sorted_res_salmon_0.025$log2fc, Bambu = both_sorted_res_bambu_0.025$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of LogFC (NDR=0.025)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.

NDR 0.05

# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.05
res_salmon_0.05 <- DTU(salmon_0.05, txdf, "salmon_0.05.", n = 3, n.small = 3)

   2    3    4    5    6    7    8    9 
5251 2903 1216  434  114   29    8    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

32 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 1468
[1] 2436

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID        featureID.1          groupID.1
95   ENSG00000010626 ENST00000007969 ENST00000007969.12 ENSG00000010626.15
96   ENSG00000010626 ENST00000323702  ENST00000323702.9 ENSG00000010626.15
97   ENSG00000010626 ENST00000428946  ENST00000428946.5 ENSG00000010626.15
98   ENSG00000010626 ENST00000433346  ENST00000433346.5 ENSG00000010626.15
99   ENSG00000010626 ENST00000451681  ENST00000451681.5 ENSG00000010626.15
4244 ENSG00000205571 ENST00000380743  ENST00000380743.9 ENSG00000205571.14
           gene transcript
95   0.04990835 0.05492203
96   0.04990835 1.00000000
97   0.04990835 0.93057242
98   0.04990835 1.00000000
99   0.04990835 1.00000000
4244 0.04987648 0.38058073
                     gid               tid day0.rep1 day0.rep2 day0.rep3
11192 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
11193 ENSG00000010671.17 ENST00000621635.4  34.30906  18.37431  21.88094
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
11192   3.85061   62.5304  915.4657 849.401157 2210.68147 2283.87095 1189.58092
11193  33.69284    0.0000    0.0000   8.479878   57.93361   28.49359   46.63524
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11192 1114.45344    34.30906    18.37431    21.88094    33.69284      0.0000
11193   41.64624     0.00000     0.00000     0.00000     3.85061     62.5304
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11192      0.0000    8.479878    57.93361    28.49359
11193    915.4657  849.401157  2210.68147  2283.87095
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.374312
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.880936
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.850610
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.692839
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.530403
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.465737
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.401157
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.479878
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.933607
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.493592
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.635242
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.646242
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.374312
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.880936
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.850610
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.692839
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.530403
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.465737
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.401157
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.479878
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.933607
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.493592
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.635242
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.646242

                     gid               tid day0.rep1 day0.rep2 day0.rep3
11192 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
11193 ENSG00000010671.17 ENST00000621635.4  34.30906  18.37431  21.88094
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
11192   3.85061   62.5304  915.4657 849.401157 2210.68147 2283.87095 1189.58092
11193  33.69284    0.0000    0.0000   8.479878   57.93361   28.49359   46.63524
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11192 1114.45344    34.30906    18.37431    21.88094    33.69284      0.0000
11193   41.64624     0.00000     0.00000     0.00000     3.85061     62.5304
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11192      0.0000    8.479878    57.93361    28.49359
11193    915.4657  849.401157  2210.68147  2283.87095
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.374312
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.880936
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.850610
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.692839
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.530403
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.465737
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.401157
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.479878
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.933607
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.493592
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.635242
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.646242
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.374312
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.880936
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.850610
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.692839
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.530403
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.465737
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.401157
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.479878
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.933607
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.493592
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.635242
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.646242

res_bambu_0.05 <- DTU(bambu_0.05, txdf,  "bambu_0.05.", n = 3, n.small = 3)

   2    3    4    5    6    7    8 
4650 1715  593  161   40    9    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

10 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 3217
[1] 7087

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID       featureID.1          groupID.1
7936 ENSG00000215252 ENST00000342314 ENST00000342314.9 ENSG00000215252.12
7937 ENSG00000215252 ENST00000484716 ENST00000484716.5 ENSG00000215252.12
7938 ENSG00000215252 ENST00000569100 ENST00000569100.5 ENSG00000215252.12
7939 ENSG00000215252 ENST00000683415 ENST00000683415.1 ENSG00000215252.12
8349 ENSG00000245275 ENST00000501280 ENST00000501280.4  ENSG00000245275.8
8350 ENSG00000245275 ENST00000522312 ENST00000522312.1  ENSG00000245275.8
           gene transcript
7936 0.04996308  0.0402418
7937 0.04996308  0.2496524
7938 0.04996308  1.0000000
7939 0.04996308  0.1464222
8349 0.04910182  0.0000000
8350 0.04910182  0.0000000
               gid        tid day0.rep1 day0.rep2 day0.rep3 day1.rep1 day2.rep1
484 BambuGene96616 BambuTx435  2.793872   6.77563  12.84754  2.946682  44.86370
485 BambuGene96616 BambuTx470 42.839368 103.32836  85.34439 21.608999  24.15738
     day3.rep1   day3.rep2    day4.rep1  day5.rep1   day5.rep2  day5.rep3
484 487.199975 952.8257672 1252.7550454 5768.24595 5685.838667 3370.87261
485   1.282105   0.9537795    0.9012626    1.03522    3.170689    4.08096
    day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1 day3.rep1.1
484   42.839368   103.32836    85.34439   21.608999    24.15738    1.282105
485    2.793872     6.77563    12.84754    2.946682    44.86370  487.199975
    day3.rep2.1  day4.rep1.1 day5.rep1.1
484   0.9537795    0.9012626     1.03522
485 952.8257672 1252.7550454  5768.24595
   sample_id day            gid        tid        value
1  day0.rep1   0 BambuGene96616 BambuTx470   42.8393679
2  day0.rep1   0 BambuGene96616 BambuTx435    2.7938718
3  day0.rep2   0 BambuGene96616 BambuTx435    6.7756300
4  day0.rep2   0 BambuGene96616 BambuTx470  103.3283572
5  day0.rep3   0 BambuGene96616 BambuTx435   12.8475432
6  day0.rep3   0 BambuGene96616 BambuTx470   85.3443940
7  day1.rep1   1 BambuGene96616 BambuTx435    2.9466817
8  day1.rep1   1 BambuGene96616 BambuTx470   21.6089989
9  day2.rep1   2 BambuGene96616 BambuTx435   44.8637024
10 day2.rep1   2 BambuGene96616 BambuTx470   24.1573782
11 day3.rep1   3 BambuGene96616 BambuTx435  487.1999748
12 day3.rep1   3 BambuGene96616 BambuTx470    1.2821052
13 day3.rep2   3 BambuGene96616 BambuTx435  952.8257672
14 day3.rep2   3 BambuGene96616 BambuTx470    0.9537795
15 day4.rep1   4 BambuGene96616 BambuTx470    0.9012626
16 day4.rep1   4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1   5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1   5 BambuGene96616 BambuTx470    1.0352200
19 day5.rep2   5 BambuGene96616 BambuTx470    3.1706893
20 day5.rep2   5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3   5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3   5 BambuGene96616 BambuTx470    4.0809596
   sample_id day            gid        tid        value
1  day0.rep1   0 BambuGene96616 BambuTx470   42.8393679
2  day0.rep1   0 BambuGene96616 BambuTx435    2.7938718
3  day0.rep2   0 BambuGene96616 BambuTx435    6.7756300
4  day0.rep2   0 BambuGene96616 BambuTx470  103.3283572
5  day0.rep3   0 BambuGene96616 BambuTx435   12.8475432
6  day0.rep3   0 BambuGene96616 BambuTx470   85.3443940
7  day1.rep1   1 BambuGene96616 BambuTx435    2.9466817
8  day1.rep1   1 BambuGene96616 BambuTx470   21.6089989
9  day2.rep1   2 BambuGene96616 BambuTx435   44.8637024
10 day2.rep1   2 BambuGene96616 BambuTx470   24.1573782
11 day3.rep1   3 BambuGene96616 BambuTx435  487.1999748
12 day3.rep1   3 BambuGene96616 BambuTx470    1.2821052
13 day3.rep2   3 BambuGene96616 BambuTx435  952.8257672
14 day3.rep2   3 BambuGene96616 BambuTx470    0.9537795
15 day4.rep1   4 BambuGene96616 BambuTx470    0.9012626
16 day4.rep1   4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1   5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1   5 BambuGene96616 BambuTx470    1.0352200
19 day5.rep2   5 BambuGene96616 BambuTx470    3.1706893
20 day5.rep2   5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3   5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3   5 BambuGene96616 BambuTx470    4.0809596

               gid        tid day0.rep1 day0.rep2 day0.rep3 day1.rep1 day2.rep1
484 BambuGene96616 BambuTx435  2.793872   6.77563  12.84754  2.946682  44.86370
485 BambuGene96616 BambuTx470 42.839368 103.32836  85.34439 21.608999  24.15738
     day3.rep1   day3.rep2    day4.rep1  day5.rep1   day5.rep2  day5.rep3
484 487.199975 952.8257672 1252.7550454 5768.24595 5685.838667 3370.87261
485   1.282105   0.9537795    0.9012626    1.03522    3.170689    4.08096
    day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1 day3.rep1.1
484   42.839368   103.32836    85.34439   21.608999    24.15738    1.282105
485    2.793872     6.77563    12.84754    2.946682    44.86370  487.199975
    day3.rep2.1  day4.rep1.1 day5.rep1.1
484   0.9537795    0.9012626     1.03522
485 952.8257672 1252.7550454  5768.24595
   sample_id day            gid        tid        value
1  day0.rep1   0 BambuGene96616 BambuTx470   42.8393679
2  day0.rep1   0 BambuGene96616 BambuTx435    2.7938718
3  day0.rep2   0 BambuGene96616 BambuTx435    6.7756300
4  day0.rep2   0 BambuGene96616 BambuTx470  103.3283572
5  day0.rep3   0 BambuGene96616 BambuTx435   12.8475432
6  day0.rep3   0 BambuGene96616 BambuTx470   85.3443940
7  day1.rep1   1 BambuGene96616 BambuTx435    2.9466817
8  day1.rep1   1 BambuGene96616 BambuTx470   21.6089989
9  day2.rep1   2 BambuGene96616 BambuTx435   44.8637024
10 day2.rep1   2 BambuGene96616 BambuTx470   24.1573782
11 day3.rep1   3 BambuGene96616 BambuTx435  487.1999748
12 day3.rep1   3 BambuGene96616 BambuTx470    1.2821052
13 day3.rep2   3 BambuGene96616 BambuTx435  952.8257672
14 day3.rep2   3 BambuGene96616 BambuTx470    0.9537795
15 day4.rep1   4 BambuGene96616 BambuTx470    0.9012626
16 day4.rep1   4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1   5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1   5 BambuGene96616 BambuTx470    1.0352200
19 day5.rep2   5 BambuGene96616 BambuTx470    3.1706893
20 day5.rep2   5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3   5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3   5 BambuGene96616 BambuTx470    4.0809596
   sample_id day            gid        tid        value
1  day0.rep1   0 BambuGene96616 BambuTx470   42.8393679
2  day0.rep1   0 BambuGene96616 BambuTx435    2.7938718
3  day0.rep2   0 BambuGene96616 BambuTx435    6.7756300
4  day0.rep2   0 BambuGene96616 BambuTx470  103.3283572
5  day0.rep3   0 BambuGene96616 BambuTx435   12.8475432
6  day0.rep3   0 BambuGene96616 BambuTx470   85.3443940
7  day1.rep1   1 BambuGene96616 BambuTx435    2.9466817
8  day1.rep1   1 BambuGene96616 BambuTx470   21.6089989
9  day2.rep1   2 BambuGene96616 BambuTx435   44.8637024
10 day2.rep1   2 BambuGene96616 BambuTx470   24.1573782
11 day3.rep1   3 BambuGene96616 BambuTx435  487.1999748
12 day3.rep1   3 BambuGene96616 BambuTx470    1.2821052
13 day3.rep2   3 BambuGene96616 BambuTx435  952.8257672
14 day3.rep2   3 BambuGene96616 BambuTx470    0.9537795
15 day4.rep1   4 BambuGene96616 BambuTx470    0.9012626
16 day4.rep1   4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1   5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1   5 BambuGene96616 BambuTx470    1.0352200
19 day5.rep2   5 BambuGene96616 BambuTx470    3.1706893
20 day5.rep2   5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3   5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3   5 BambuGene96616 BambuTx470    4.0809596

confirmed_salmon_0.05 <- res_salmon_0.05[res_salmon_0.05$transcript < 0.05, ]
nrow(confirmed_salmon_0.05)

[1] 2375

confirmed_bambu_0.05 <- res_bambu_0.05[res_bambu_0.05$transcript < 0.05, ]
nrow(confirmed_bambu_0.05)

[1] 6427

For Illumina+Salmon, out of the 9958 tested genes and 27223 tested features, DEXSeq test identified 1468 genes showing evidence of isoform switching involving 2436 transcripts. For PacBio+Bambu out of the 7171 tested genes and 17949 tested features, 3217 genes involving 7087 trancsripts were identified.

After the stageR procedure, 2375 transcripts passed the confirmation stage for Illumina+Salmon and 6427 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.

Upset Plot

# Screened Genes
length(intersect(confirmed_salmon_0.05$GeneID, confirmed_bambu_0.05$GeneID))

[1] 752

venn <- list(SALMON = confirmed_salmon_0.05$GeneID, BAMBU = confirmed_bambu_0.05$GeneID)
ggvenn(venn)

upset(fromList(venn))

# Confirmed Transcripts
length(intersect(confirmed_salmon_0.05$TranscriptID, confirmed_bambu_0.05$TranscriptID))

[1] 844

venn <- list(SALMON = confirmed_salmon_0.05$TranscriptID, BAMBU = confirmed_bambu_0.05$TranscriptID)
ggvenn(venn)

upset(fromList(venn))

From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 11 %.

Comparsion of pAdj and logFC

both_detected <-
  intersect(res_bambu_0.05$TranscriptID, res_salmon_0.05$TranscriptID)
sorted_res_salmon_0.05 <- res_salmon_0.05[order(res_salmon_0.05$TranscriptID),]
both_sorted_res_salmon_0.05 <- sorted_res_salmon_0.05[which(sorted_res_salmon_0.05$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.05 <- res_bambu_0.05[order(res_bambu_0.05$TranscriptID),]
both_sorted_res_bambu_0.05 <- sorted_res_bambu_0.05[which(sorted_res_bambu_0.05$TranscriptID %in% both_detected), ]

padj <- data.frame(Salmon = both_sorted_res_salmon_0.05$transcript, Bambu = both_sorted_res_bambu_0.05$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of P-values (NDR=0.05)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

Warning: Removed 667 rows containing non-finite values (`stat_smooth()`).

logfc <- data.frame(Salmon = both_sorted_res_salmon_0.05$log2fc, Bambu = both_sorted_res_bambu_0.05$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of LogFC (NDR=0.05)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.

NDR 0.1

# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.1
res_salmon_0.1 <- DTU(salmon_0.1, txdf, "salmon_0.1.", n = 3, n.small = 3)

   2    3    4    5    6    7    8    9 
5292 2929 1228  448  116   28    8    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

27 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 1507
[1] 2505

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID        featureID.1          groupID.1
1799 ENSG00000130714 ENST00000341012 ENST00000341012.13 ENSG00000130714.19
1800 ENSG00000130714 ENST00000402686  ENST00000402686.8 ENSG00000130714.19
1801 ENSG00000130714 ENST00000683392  ENST00000683392.1 ENSG00000130714.19
4555 ENSG00000233822 ENST00000606613  ENST00000606613.1  ENSG00000233822.6
4556 ENSG00000233822 ENST00000612898  ENST00000612898.2  ENSG00000233822.6
3696 ENSG00000175287 ENST00000308941  ENST00000308941.9 ENSG00000175287.19
           gene transcript
1799 0.04974351 1.00000000
1800 0.04974351 1.00000000
1801 0.04974351 0.01820608
4555 0.04973010 0.00000000
4556 0.04973010 0.00000000
3696 0.04972740 1.00000000
                     gid               tid day0.rep1 day0.rep2 day0.rep3
11897 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
11898 ENSG00000010671.17 ENST00000621635.4  34.30906  18.38182  21.87258
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
11897  3.848584  62.53679  915.4419 849.164288 2211.61114 2285.02984 1189.65518
11898 33.675107   0.00000    0.0000   8.477514   57.95797   28.50805   46.63815
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11897 1114.87293    34.30906    18.38182    21.87258   33.675107     0.00000
11898   41.66192     0.00000     0.00000     0.00000    3.848584    62.53679
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11897      0.0000    8.477514    57.95797    28.50805
11898    915.4419  849.164288  2211.61114  2285.02984
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.381821
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.872575
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.848584
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.675107
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.536788
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.441938
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.164288
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.477514
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.957970
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.508050
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.638153
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.661918
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.381821
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.872575
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.848584
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.675107
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.536788
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.441938
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.164288
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.477514
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.957970
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.508050
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.638153
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.661918

                     gid               tid day0.rep1 day0.rep2 day0.rep3
11897 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
11898 ENSG00000010671.17 ENST00000621635.4  34.30906  18.38182  21.87258
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
11897  3.848584  62.53679  915.4419 849.164288 2211.61114 2285.02984 1189.65518
11898 33.675107   0.00000    0.0000   8.477514   57.95797   28.50805   46.63815
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11897 1114.87293    34.30906    18.38182    21.87258   33.675107     0.00000
11898   41.66192     0.00000     0.00000     0.00000    3.848584    62.53679
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11897      0.0000    8.477514    57.95797    28.50805
11898    915.4419  849.164288  2211.61114  2285.02984
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.381821
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.872575
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.848584
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.675107
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.536788
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.441938
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.164288
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.477514
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.957970
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.508050
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.638153
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.661918
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.309065
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.381821
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.872575
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.848584
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.675107
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.536788
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  915.441938
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  849.164288
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.477514
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.957970
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.508050
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.638153
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.661918

res_bambu_0.1 <- DTU(bambu_0.1, txdf,  "bambu_0.1.", n = 3, n.small = 3)

   2    3    4    5    6    7    8 
4767 1774  610  163   41    8    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

9 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 3316
[1] 7332

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID       featureID.1          groupID.1
3089 ENSG00000128487 ENST00000395530 ENST00000395530.6 ENSG00000128487.19
3090 ENSG00000128487 ENST00000581399 ENST00000581399.6 ENSG00000128487.19
4725 ENSG00000151806      BambuTx299        BambuTx299 ENSG00000151806.14
4726 ENSG00000151806 ENST00000281543 ENST00000281543.6 ENSG00000151806.14
4670 ENSG00000150672 ENST00000376104 ENST00000376104.7 ENSG00000150672.18
4671 ENSG00000150672 ENST00000398309 ENST00000398309.6 ENSG00000150672.18
           gene transcript
3089 0.04996015  0.0000000
3090 0.04996015  0.0000000
4725 0.04972857  0.0000000
4726 0.04972857  0.0000000
4670 0.04953250  0.8551188
4671 0.04953250  0.8294748
               gid         tid day0.rep1  day0.rep2 day0.rep3 day1.rep1
233 BambuGene96616 BambuTx1180  2.785771   6.775579  12.84737  2.945325
234 BambuGene96616 BambuTx1181 42.715158 103.327582  85.34327 21.599052
    day2.rep1  day3.rep1   day3.rep2    day4.rep1   day5.rep1   day5.rep2
233  45.25648 485.459573 954.2535645 1252.4865423 5764.766530 5691.780908
234  24.36887   1.277525   0.9552088    0.9010695    1.034596    3.174003
      day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
233 3358.146591   42.715158  103.327582    85.34327   21.599052    24.36887
234    4.065553    2.785771    6.775579    12.84737    2.945325    45.25648
    day3.rep1.1 day3.rep2.1  day4.rep1.1 day5.rep1.1
233    1.277525   0.9552088    0.9010695    1.034596
234  485.459573 954.2535645 1252.4865423 5764.766530
   sample_id day            gid         tid        value
1  day0.rep1   0 BambuGene96616 BambuTx1181   42.7151581
2  day0.rep1   0 BambuGene96616 BambuTx1180    2.7857712
3  day0.rep2   0 BambuGene96616 BambuTx1180    6.7755791
4  day0.rep2   0 BambuGene96616 BambuTx1181  103.3275817
5  day0.rep3   0 BambuGene96616 BambuTx1180   12.8473740
6  day0.rep3   0 BambuGene96616 BambuTx1181   85.3432698
7  day1.rep1   1 BambuGene96616 BambuTx1180    2.9453252
8  day1.rep1   1 BambuGene96616 BambuTx1181   21.5990517
9  day2.rep1   2 BambuGene96616 BambuTx1180   45.2564765
10 day2.rep1   2 BambuGene96616 BambuTx1181   24.3688720
11 day3.rep1   3 BambuGene96616 BambuTx1180  485.4595730
12 day3.rep1   3 BambuGene96616 BambuTx1181    1.2775252
13 day3.rep2   3 BambuGene96616 BambuTx1180  954.2535645
14 day3.rep2   3 BambuGene96616 BambuTx1181    0.9552088
15 day4.rep1   4 BambuGene96616 BambuTx1181    0.9010695
16 day4.rep1   4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1   5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1   5 BambuGene96616 BambuTx1181    1.0345956
19 day5.rep2   5 BambuGene96616 BambuTx1181    3.1740030
20 day5.rep2   5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3   5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3   5 BambuGene96616 BambuTx1181    4.0655528
   sample_id day            gid         tid        value
1  day0.rep1   0 BambuGene96616 BambuTx1181   42.7151581
2  day0.rep1   0 BambuGene96616 BambuTx1180    2.7857712
3  day0.rep2   0 BambuGene96616 BambuTx1180    6.7755791
4  day0.rep2   0 BambuGene96616 BambuTx1181  103.3275817
5  day0.rep3   0 BambuGene96616 BambuTx1180   12.8473740
6  day0.rep3   0 BambuGene96616 BambuTx1181   85.3432698
7  day1.rep1   1 BambuGene96616 BambuTx1180    2.9453252
8  day1.rep1   1 BambuGene96616 BambuTx1181   21.5990517
9  day2.rep1   2 BambuGene96616 BambuTx1180   45.2564765
10 day2.rep1   2 BambuGene96616 BambuTx1181   24.3688720
11 day3.rep1   3 BambuGene96616 BambuTx1180  485.4595730
12 day3.rep1   3 BambuGene96616 BambuTx1181    1.2775252
13 day3.rep2   3 BambuGene96616 BambuTx1180  954.2535645
14 day3.rep2   3 BambuGene96616 BambuTx1181    0.9552088
15 day4.rep1   4 BambuGene96616 BambuTx1181    0.9010695
16 day4.rep1   4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1   5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1   5 BambuGene96616 BambuTx1181    1.0345956
19 day5.rep2   5 BambuGene96616 BambuTx1181    3.1740030
20 day5.rep2   5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3   5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3   5 BambuGene96616 BambuTx1181    4.0655528

               gid         tid day0.rep1  day0.rep2 day0.rep3 day1.rep1
233 BambuGene96616 BambuTx1180  2.785771   6.775579  12.84737  2.945325
234 BambuGene96616 BambuTx1181 42.715158 103.327582  85.34327 21.599052
    day2.rep1  day3.rep1   day3.rep2    day4.rep1   day5.rep1   day5.rep2
233  45.25648 485.459573 954.2535645 1252.4865423 5764.766530 5691.780908
234  24.36887   1.277525   0.9552088    0.9010695    1.034596    3.174003
      day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
233 3358.146591   42.715158  103.327582    85.34327   21.599052    24.36887
234    4.065553    2.785771    6.775579    12.84737    2.945325    45.25648
    day3.rep1.1 day3.rep2.1  day4.rep1.1 day5.rep1.1
233    1.277525   0.9552088    0.9010695    1.034596
234  485.459573 954.2535645 1252.4865423 5764.766530
   sample_id day            gid         tid        value
1  day0.rep1   0 BambuGene96616 BambuTx1181   42.7151581
2  day0.rep1   0 BambuGene96616 BambuTx1180    2.7857712
3  day0.rep2   0 BambuGene96616 BambuTx1180    6.7755791
4  day0.rep2   0 BambuGene96616 BambuTx1181  103.3275817
5  day0.rep3   0 BambuGene96616 BambuTx1180   12.8473740
6  day0.rep3   0 BambuGene96616 BambuTx1181   85.3432698
7  day1.rep1   1 BambuGene96616 BambuTx1180    2.9453252
8  day1.rep1   1 BambuGene96616 BambuTx1181   21.5990517
9  day2.rep1   2 BambuGene96616 BambuTx1180   45.2564765
10 day2.rep1   2 BambuGene96616 BambuTx1181   24.3688720
11 day3.rep1   3 BambuGene96616 BambuTx1180  485.4595730
12 day3.rep1   3 BambuGene96616 BambuTx1181    1.2775252
13 day3.rep2   3 BambuGene96616 BambuTx1180  954.2535645
14 day3.rep2   3 BambuGene96616 BambuTx1181    0.9552088
15 day4.rep1   4 BambuGene96616 BambuTx1181    0.9010695
16 day4.rep1   4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1   5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1   5 BambuGene96616 BambuTx1181    1.0345956
19 day5.rep2   5 BambuGene96616 BambuTx1181    3.1740030
20 day5.rep2   5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3   5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3   5 BambuGene96616 BambuTx1181    4.0655528
   sample_id day            gid         tid        value
1  day0.rep1   0 BambuGene96616 BambuTx1181   42.7151581
2  day0.rep1   0 BambuGene96616 BambuTx1180    2.7857712
3  day0.rep2   0 BambuGene96616 BambuTx1180    6.7755791
4  day0.rep2   0 BambuGene96616 BambuTx1181  103.3275817
5  day0.rep3   0 BambuGene96616 BambuTx1180   12.8473740
6  day0.rep3   0 BambuGene96616 BambuTx1181   85.3432698
7  day1.rep1   1 BambuGene96616 BambuTx1180    2.9453252
8  day1.rep1   1 BambuGene96616 BambuTx1181   21.5990517
9  day2.rep1   2 BambuGene96616 BambuTx1180   45.2564765
10 day2.rep1   2 BambuGene96616 BambuTx1181   24.3688720
11 day3.rep1   3 BambuGene96616 BambuTx1180  485.4595730
12 day3.rep1   3 BambuGene96616 BambuTx1181    1.2775252
13 day3.rep2   3 BambuGene96616 BambuTx1180  954.2535645
14 day3.rep2   3 BambuGene96616 BambuTx1181    0.9552088
15 day4.rep1   4 BambuGene96616 BambuTx1181    0.9010695
16 day4.rep1   4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1   5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1   5 BambuGene96616 BambuTx1181    1.0345956
19 day5.rep2   5 BambuGene96616 BambuTx1181    3.1740030
20 day5.rep2   5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3   5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3   5 BambuGene96616 BambuTx1181    4.0655528

confirmed_salmon_0.1 <- res_salmon_0.1[res_salmon_0.1$transcript < 0.05, ]
nrow(confirmed_salmon_0.1)

[1] 2430

confirmed_bambu_0.1 <- res_bambu_0.1[res_bambu_0.1$transcript < 0.05, ]
nrow(confirmed_bambu_0.1)

[1] 6661

For Illumina+Salmon, out of the 10052 tested genes and 27506 tested features, DEXSeq test identified 1507 genes showing evidence of isoform switching involving 2505 transcripts. For PacBio+Bambu out of the 7366 tested genes and 18437 tested features, 3316 genes involving 7332 trancsripts were identified.

After the stageR procedure, 2430 transcripts passed the confirmation stage for Illumina+Salmon and 6661 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.

Upset Plot

# Screened Genes
length(intersect(confirmed_salmon_0.1$GeneID, confirmed_bambu_0.1$GeneID))

[1] 779

venn <- list(SALMON = confirmed_salmon_0.1$GeneID, BAMBU = confirmed_bambu_0.1$GeneID)
ggvenn(venn)

upset(fromList(venn))

# Confirmed Transcripts
length(intersect(confirmed_salmon_0.1$TranscriptID, confirmed_bambu_0.1$TranscriptID))

[1] 879

venn <- list(SALMON = confirmed_salmon_0.1$TranscriptID, BAMBU = confirmed_bambu_0.1$TranscriptID)
ggvenn(venn)

upset(fromList(venn))

From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 11 %.

Comparsion of pAdj and logFC

both_detected <-
  intersect(res_bambu_0.1$TranscriptID, res_salmon_0.1$TranscriptID)
sorted_res_salmon_0.1 <- res_salmon_0.1[order(res_salmon_0.1$TranscriptID),]
both_sorted_res_salmon_0.1 <- sorted_res_salmon_0.1[which(sorted_res_salmon_0.1$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.1 <- res_bambu_0.1[order(res_bambu_0.1$TranscriptID),]
both_sorted_res_bambu_0.1 <- sorted_res_bambu_0.1[which(sorted_res_bambu_0.1$TranscriptID %in% both_detected), ]

padj <- data.frame(Salmon = both_sorted_res_salmon_0.1$transcript, Bambu = both_sorted_res_bambu_0.1$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of P-values (NDR=0.1)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

Warning: Removed 662 rows containing non-finite values (`stat_smooth()`).

logfc <- data.frame(Salmon = both_sorted_res_salmon_0.1$log2fc, Bambu = both_sorted_res_bambu_0.1$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of LogFC (NDR=0.1)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).

The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.

NDR 0.2

# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.2
res_salmon_0.2 <- DTU(salmon_0.2, txdf, "salmon_0.2.", n = 3, n.small = 3)

   2    3    4    5    6    7    8    9 
5393 3052 1297  467  115   31    6    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

28 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 1578
[1] 2569

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID       featureID.1          groupID.1
318  ENSG00000064313 ENST00000378164 ENST00000378164.7 ENSG00000064313.13
319  ENSG00000064313 ENST00000686879 ENST00000686879.1 ENSG00000064313.13
4464 ENSG00000198838 ENST00000389232 ENST00000389232.9 ENSG00000198838.14
4465 ENSG00000198838 ENST00000415757 ENST00000415757.7 ENSG00000198838.14
4466 ENSG00000198838 ENST00000634418 ENST00000634418.1 ENSG00000198838.14
4467 ENSG00000198838 ENST00000634730 ENST00000634730.1 ENSG00000198838.14
           gene transcript
318  0.04985152          0
319  0.04985152          0
4464 0.04982910          1
4465 0.04982910          1
4466 0.04982910          1
4467 0.04982910          1
                     gid               tid day0.rep1 day0.rep2 day0.rep3
13929 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
13930 ENSG00000010671.17 ENST00000621635.4  34.28343  18.35999  21.86282
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
13929  3.846644  62.47691  913.4393 848.918664 2209.66400 2287.05736 1190.06724
13930 33.658133   0.00000    0.0000   8.475062   57.90694   28.53335   46.65431
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
13929 1114.41512    34.28343    18.35999    21.86282   33.658133     0.00000
13930   41.67596     0.00000     0.00000     0.00000    3.846644    62.47691
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
13929      0.0000    8.475062    57.90694    28.53335
13930    913.4393  848.918664  2209.66400  2287.05736
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.283430
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.359993
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.862819
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.846644
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.658133
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.476905
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  913.439336
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  848.918664
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.475062
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.906943
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.533345
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.654307
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.675958
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.283430
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.359993
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.862819
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.846644
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.658133
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.476905
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  913.439336
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  848.918664
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.475062
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.906943
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.533345
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.654307
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.675958

                     gid               tid day0.rep1 day0.rep2 day0.rep3
13929 ENSG00000010671.17 ENST00000308731.8   0.00000   0.00000   0.00000
13930 ENSG00000010671.17 ENST00000621635.4  34.28343  18.35999  21.86282
      day1.rep1 day2.rep1 day3.rep1  day3.rep2  day4.rep1  day5.rep1  day5.rep2
13929  3.846644  62.47691  913.4393 848.918664 2209.66400 2287.05736 1190.06724
13930 33.658133   0.00000    0.0000   8.475062   57.90694   28.53335   46.65431
       day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
13929 1114.41512    34.28343    18.35999    21.86282   33.658133     0.00000
13930   41.67596     0.00000     0.00000     0.00000    3.846644    62.47691
      day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
13929      0.0000    8.475062    57.90694    28.53335
13930    913.4393  848.918664  2209.66400  2287.05736
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.283430
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.359993
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.862819
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.846644
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.658133
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.476905
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  913.439336
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  848.918664
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.475062
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.906943
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.533345
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.654307
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.675958
   sample_id day                gid               tid       value
1  day0.rep1   0 ENSG00000010671.17 ENST00000621635.4   34.283430
2  day0.rep1   0 ENSG00000010671.17 ENST00000308731.8    0.000000
3  day0.rep2   0 ENSG00000010671.17 ENST00000308731.8    0.000000
4  day0.rep2   0 ENSG00000010671.17 ENST00000621635.4   18.359993
5  day0.rep3   0 ENSG00000010671.17 ENST00000308731.8    0.000000
6  day0.rep3   0 ENSG00000010671.17 ENST00000621635.4   21.862819
7  day1.rep1   1 ENSG00000010671.17 ENST00000308731.8    3.846644
8  day1.rep1   1 ENSG00000010671.17 ENST00000621635.4   33.658133
9  day2.rep1   2 ENSG00000010671.17 ENST00000308731.8   62.476905
10 day2.rep1   2 ENSG00000010671.17 ENST00000621635.4    0.000000
11 day3.rep1   3 ENSG00000010671.17 ENST00000308731.8  913.439336
12 day3.rep1   3 ENSG00000010671.17 ENST00000621635.4    0.000000
13 day3.rep2   3 ENSG00000010671.17 ENST00000308731.8  848.918664
14 day3.rep2   3 ENSG00000010671.17 ENST00000621635.4    8.475062
15 day4.rep1   4 ENSG00000010671.17 ENST00000621635.4   57.906943
16 day4.rep1   4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1   5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1   5 ENSG00000010671.17 ENST00000621635.4   28.533345
19 day5.rep2   5 ENSG00000010671.17 ENST00000621635.4   46.654307
20 day5.rep2   5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3   5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3   5 ENSG00000010671.17 ENST00000621635.4   41.675958

res_bambu_0.2 <- DTU(bambu_0.2, txdf,  "bambu_0.2.", n = 3, n.small = 3)

   2    3    4    5    6    7    8 
4966 1960  673  191   45    9    3 

converting counts to integer mode

Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors

11 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT

[1] 3530
[1] 7799

The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run. 

             groupID       featureID        featureID.1          groupID.1
5737 ENSG00000162614 ENST00000330010 ENST00000330010.12 ENSG00000162614.19
5738 ENSG00000162614 ENST00000334785 ENST00000334785.12 ENSG00000162614.19
5739 ENSG00000162614 ENST00000401035  ENST00000401035.7 ENSG00000162614.19
8363 ENSG00000198774     BambuTx2106        BambuTx2106  ENSG00000198774.5
8364 ENSG00000198774 ENST00000361228  ENST00000361228.5  ENSG00000198774.5
7218 ENSG00000180879     BambuTx3324        BambuTx3324 ENSG00000180879.14
           gene transcript
5737 0.04987062 0.01990172
5738 0.04987062 0.71463240
5739 0.04987062 0.66990944
8363 0.04986906 0.00000000
8364 0.04986906 0.00000000
7218 0.04982645 0.00000000
                    gid                tid day0.rep1 day0.rep2 day0.rep3
7024 ENSG00000004864.14 ENST00000265631.10  2346.627  1944.294  2181.709
7025 ENSG00000004864.14  ENST00000416240.6  2940.430  2123.040  2312.630
     day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
7024  2009.438  3398.837  2367.424  2374.237  1881.663     0.000     0.000
7025  2696.543  3398.837  2561.099  2374.237  1881.663  3190.367  3430.594
     day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
7024     0.000    2940.430    2123.040    2312.630    2696.543    3398.837
7025  2955.513    2346.627    1944.294    2181.709    2009.438    3398.837
     day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
7024    2561.099    2374.237    1881.663    3190.367
7025    2367.424    2374.237    1881.663       0.000
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2940.430
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2346.627
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1944.294
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.040
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2181.709
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2312.630
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2009.438
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2696.543
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3398.837
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2561.099
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2374.237
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1881.663
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3190.367
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3430.594
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2955.513
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2940.430
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2346.627
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1944.294
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.040
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2181.709
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2312.630
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2009.438
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2696.543
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3398.837
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2561.099
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2374.237
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1881.663
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3190.367
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3430.594
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2955.513

                    gid                tid day0.rep1 day0.rep2 day0.rep3
7024 ENSG00000004864.14 ENST00000265631.10  2346.627  1944.294  2181.709
7025 ENSG00000004864.14  ENST00000416240.6  2940.430  2123.040  2312.630
     day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
7024  2009.438  3398.837  2367.424  2374.237  1881.663     0.000     0.000
7025  2696.543  3398.837  2561.099  2374.237  1881.663  3190.367  3430.594
     day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
7024     0.000    2940.430    2123.040    2312.630    2696.543    3398.837
7025  2955.513    2346.627    1944.294    2181.709    2009.438    3398.837
     day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
7024    2561.099    2374.237    1881.663    3190.367
7025    2367.424    2374.237    1881.663       0.000
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2940.430
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2346.627
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1944.294
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.040
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2181.709
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2312.630
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2009.438
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2696.543
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3398.837
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2561.099
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2374.237
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1881.663
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3190.367
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3430.594
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2955.513
   sample_id day                gid                tid    value
1  day0.rep1   0 ENSG00000004864.14  ENST00000416240.6 2940.430
2  day0.rep1   0 ENSG00000004864.14 ENST00000265631.10 2346.627
3  day0.rep2   0 ENSG00000004864.14 ENST00000265631.10 1944.294
4  day0.rep2   0 ENSG00000004864.14  ENST00000416240.6 2123.040
5  day0.rep3   0 ENSG00000004864.14 ENST00000265631.10 2181.709
6  day0.rep3   0 ENSG00000004864.14  ENST00000416240.6 2312.630
7  day1.rep1   1 ENSG00000004864.14 ENST00000265631.10 2009.438
8  day1.rep1   1 ENSG00000004864.14  ENST00000416240.6 2696.543
9  day2.rep1   2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1   2 ENSG00000004864.14  ENST00000416240.6 3398.837
11 day3.rep1   3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1   3 ENSG00000004864.14  ENST00000416240.6 2561.099
13 day3.rep2   3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2   3 ENSG00000004864.14  ENST00000416240.6 2374.237
15 day4.rep1   4 ENSG00000004864.14  ENST00000416240.6 1881.663
16 day4.rep1   4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1   5 ENSG00000004864.14 ENST00000265631.10    0.000
18 day5.rep1   5 ENSG00000004864.14  ENST00000416240.6 3190.367
19 day5.rep2   5 ENSG00000004864.14  ENST00000416240.6 3430.594
20 day5.rep2   5 ENSG00000004864.14 ENST00000265631.10    0.000
21 day5.rep3   5 ENSG00000004864.14 ENST00000265631.10    0.000
22 day5.rep3   5 ENSG00000004864.14  ENST00000416240.6 2955.513

confirmed_salmon_0.2 <- res_salmon_0.1[res_salmon_0.2$transcript < 0.05, ]
nrow(confirmed_salmon_0.2)

[1] 2528

confirmed_bambu_0.2 <- res_bambu_0.2[res_bambu_0.2$transcript < 0.05, ]
nrow(confirmed_bambu_0.2)

[1] 7108

For Illumina+Salmon, out of the 10364 tested genes and 28447 tested features, DEXSeq test identified 1578 genes showing evidence of isoform switching involving 2569 transcripts. For PacBio+Bambu out of the 7847 tested genes and 19816 tested features, 3530 genes involving 7799 trancsripts were identified.

After the stageR procedure, 2528 transcripts passed the confirmation stage for Illumina+Salmon and 7108 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.

Upset Plot

# Screened Genes
length(intersect(confirmed_salmon_0.2$GeneID, confirmed_bambu_0.2$GeneID))

[1] 697

venn <- list(SALMON = confirmed_salmon_0.2$GeneID, BAMBU = confirmed_bambu_0.2$GeneID)
ggvenn(venn)

upset(fromList(venn))

# Confirmed Transcripts
length(intersect(confirmed_salmon_0.2$TranscriptID, confirmed_bambu_0.2$TranscriptID))

[1] 654

venn <- list(SALMON = confirmed_salmon_0.2$TranscriptID, BAMBU = confirmed_bambu_0.2$TranscriptID)
ggvenn(venn)

upset(fromList(venn))

From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 7 %. This percentage is much less than for the cutoffs from before.

Comparsion of pAdj and logFC

both_detected <-
  intersect(res_bambu_0.2$TranscriptID, res_salmon_0.2$TranscriptID)
sorted_res_salmon_0.2 <- res_salmon_0.2[order(res_salmon_0.2$TranscriptID),]
both_sorted_res_salmon_0.2 <- sorted_res_salmon_0.2[which(sorted_res_salmon_0.2$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.2 <- res_bambu_0.2[order(res_bambu_0.2$TranscriptID),]
both_sorted_res_bambu_0.2 <- sorted_res_bambu_0.2[which(sorted_res_bambu_0.2$TranscriptID %in% both_detected), ]

padj <- data.frame(Salmon = both_sorted_res_salmon_0.2$transcript, Bambu = both_sorted_res_bambu_0.2$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of P-values (NDR=0.2)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

Warning: Removed 674 rows containing non-finite values (`stat_smooth()`).

logfc <- data.frame(Salmon = both_sorted_res_salmon_0.2$log2fc, Bambu = both_sorted_res_bambu_0.2$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
  geom_point() + 
  geom_smooth() +
  theme_minimal() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_color_viridis() +
  labs(title = "Comparison of LogFC (NDR=0.2)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")

`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.